https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Casimiro+SolizProteopedia - User contributions [en]2026-10-02T01:38:18ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=DNA_Repair&diff=3644279DNA Repair2022-10-18T23:47:52Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/2'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/6'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /><br />
<br />
==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
== References ==<br />
<references/></div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644272DNA Repair2022-10-18T20:50:29Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /></div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644271DNA Repair2022-10-18T20:49:06Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
== References ==<br />
<references/><br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /></div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644270DNA Repair2022-10-18T20:35:18Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /></div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644269DNA Repair2022-10-18T20:34:23Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
== References ==<br />
<references/><br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /></div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644268Sandbox reserved 17532022-10-18T20:31:44Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
== References ==<br />
<references/></div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644267Sandbox reserved 17532022-10-18T20:30:55Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/></div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644266Sandbox reserved 17532022-10-18T20:30:39Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
<br />
↑ Schormann N, Ricciardi R, Chattopadhyay D. Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes. Protein Sci. 2014 Dec;23(12):1667-85. doi: 10.1002/pro.2554. Epub 2014 Oct 25. PMID:25252105 doi:http://dx.doi.org/10.1002/pro.2554<br />
↑ Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA. Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. EMBO J. 1998 Sep 1;17(17):5214-26. PMID:9724657 doi:10.1093/emboj/17.17.5214<br />
↑ Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285 doi:http://dx.doi.org/10.1038/384087a0</div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644265DNA Repair2022-10-18T20:29:35Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /></div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644264DNA Repair2022-10-18T20:28:24Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /><br />
<br />
==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
== References ==<br />
<references/></div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644263DNA Repair2022-10-18T20:27:54Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /><br />
<br />
==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=DNA_Repair&diff=3644262DNA Repair2022-10-18T20:26:23Z<p>Casimiro Soliz: </p>
<hr />
<div> The discussion on this page is targeted at genetics students, so familiarity with [[DNA]] structure, [[DNA Replication]] and [[Basics of Protein Structure]] is assumed.<br />
<br />
'''DNA Repair''' is necessary to maintain genome fidelity. Errors in DNA can arise from many different sources. Errors introduced in the replication process are the simplest source. This leads to non-Watson-Crick base pairs and local distortions in the helix. Bases can also be damaged by oxidizing agents, alkylating agents or UV light. This page will discuss different strategies for repairing these types of DNA damage.<br />
<br />
<StructureSection load='B-DNA.pdb' size='350' side='right' scene='' caption=''><br />
<br />
==DNA Mismatch Repair by MutH==<br />
<br />
DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence. <br />
<br />
<br />
=== Structure of MutH ===<br />
MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. <br />
<br />
The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. <br />
<br />
MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.<br />
<br />
=== References ===<br />
Ban, C., & Yang, W. (1998). Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. The EMBO <br />
journal, 17(5), 1526–1534. https://doi.org/10.1093/emboj/17.5.1526<br />
<br />
Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N., & Yang, W. (2005). MutH complexed with hemi- and unmethylated DNAs: coupling base recognition <br />
and DNA cleavage. Molecular cell, 20(1), 155–166. https://doi.org/10.1016/j.molcel.2005.08.019<br />
<br />
Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Fundamentals of Biochemistry: Life at the molecular level. Wiley.<br />
<br />
<br />
<br />
<br />
==RecA Protein Structure and Function==<br />
<br />
<br />
=== Monomer Structure ===<br />
<br />
<scene name='92/925552/5_monomers/4'>RecA</scene> is one of the many proteins that is involved in recombination cross-over events and during recombination repair in response to single strand DNA breaks. RecA is a rather small monomer protein that can multiplex with itself up to thousands of RecA proteins to associate with ssDNA. The structure of RecA was determined through x-ray crystallography and each monomer contains very distinct structural components. These <scene name='92/925552/Reca_domains/4'>components</scene> are a largely helical 30-residue N-terminal region, a 240-residue α/ß ATPase core, and a 64-residue C-terminal <br />
globular domain.<br />
<br />
<br />
=== Monomer Association ===<br />
<br />
<br />
The process of recruiting new RecA monomers is carried out through an ATP-dependent process. This occurs through the binding of ATP to two adjacent <scene name='92/925552/Atpase_core/5'>α/ß ATPase cores</scene> on subsequent RecA monomers. To properly grow the crystal that was used to determine structure through x-ray crystallography, a non-hydrolyzable analog of ATP is used. This analog has the shorthand formula of ADP-AlF4-Mg. Specifically, the aluminum tetrafluoride is bound to the adenine diphosphate in the ɣ position. Several residues are involved in the hydrolysis of ATP to coordinate strand exchange after binding to ssDNA has occurred. On one of the RecA monomers, two lysine residues, Lys 248 and Lys 250, are responsible for coordinating with the ɣ phosphate stabilizing it. Lys 250 has also been implicated to have an additional function: to coordinate a glutamic acid, Glu 96, on the adjacent RecA monomer. This coordination with Glu 96 is achieved through hydrogen bonding and is believed to be critical for the catalytic mechanism. Specifically, there is a complex network of hydrogen bonding that is occurring between several other residues to rotate Glu 96 to a more favorable conformation enabling Glu 96 to act as a nucleophile.<br />
<br />
<br />
=== ssDNA Binding ===<br />
<br />
<br />
Once several RecA monomers have coordinated with one another, they coordinate with ssDNA to form a repeating structure that contains exactly three nucleotides for every RecA monomer. However, this does not mean that each nucleotide triplet only interacts with a single RecA monomer. In reality, each RecA monomer spans three nucleotides, but the nucleotide triplet interacts with the other two RecA surrounding it in both the 5' and 3' direction. Essentially, each nucleotide triplet is interacting with three different RecA monomers named RecA5', RecA0, and RecA3' based on their relative location to the nucleotide triplet. The first nucleotide of the triplet is bound by both RecA5' and RecA0, the second is bound only by Rec0 and the third is bound by both Rec0 and Rec3'. <scene name='92/925552/Phosphate_interactions/9'>Hydrogen bonding</scene> is responsible for stabilizing ssDNA within this conformation. Specifically, the phosphate backbone of the nucleotide triplet is what interacts with the RecA monomer residues through hydrogen bonding (dashed lines). Interestingly, the hydrogen bonding interactions that are occurring do not always use the side chains, but often will interact with the amide groups on amino acid backbones. For example, the first phosphate group within a nucleotide triplet will interact with the backbone amide of Met 197 from RecA5' and the amide backbone of Asn 123 from RecA0. The second phosphate of the triplet interacts with Gly 211 and Gly 212 on RecA0. The third phosphate of the triplet is unique as it interacts with the side chains of Ser 172 and Arg 176.<br />
<br />
<br />
=== Strand Exchange Mechanism ===<br />
<br />
<br />
Once a RecA filament has properly formed and coordinated with ssDNA, a complementary DNA strand must be located. Once a complementary strand is located, the donor <scene name='92/925552/Strand_exchange_2/4'>dsDNA</scene> is wound into the filament complex where the ssDNA and dsDNA form a temperate three-stranded DNA intermediate. Another protein complex, RecBCD, not modeled here, helps resolve the strand exchange process via the formation of a holiday junction. The process of strand exchange is heavily mediated through traditional Watson-Crick base pairing rules, but also by a few residues located within the RecA filament complex. Specifically, Ser 162 on each RecA monomer contacts the phosphate groups near the nucleotide triplet. Additionally, Met 164 increases the spacing between nucleotide triplets by inserting itself into the gap between them. This insertion allows for more strict base pairing stabilization. The final residue implicated in strand exchange appears to have a proofreading mechanism similar to that of DNA polymerases. This residue is <scene name='92/925552/Arg_169/2'>Arg 169</scene> and has been implicated in having base-pairing proofreading abilities by hydrogen bonding with O2 groups in thymidine bases (DT 7-9). This interaction is able to check for proper Watson-Crick base pairing because the bond lengths associated with proper base pairing will allow for proper interactions between Arg 169 and thymidine. Incorrect base pairing will cause thymidine residues to shift position preventing necessary Arg 169 interactions. This functionality has been shown through the mutation of Arg 169 to Histidine resulting in ultraviolet sensitivity and increased mismatched base pairing. However, this proofreading mechanism is not completely understood and this functionality may be a fragment of Arg 169 being able to interact with subsequent thymidine bases used in the crystalized DNA structure.<br />
<br />
== References ==<br />
<br />
1. Chen, Z., Yang, H., & Pavletich, N. P. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453(7194), 489–494. https://doi.org/10.1038/nature06971<br />
<br />
2.Voet, D., Voet, J. G., & Pratt, C. W. (2013). Fundamentals of biochemistry : life at the molecular level. Wiley.<br />
<br />
3. Yang, H., Zhou, C., Dhar, A., & Pavletich, N. P. (2020). Mechanism of strand exchange from RecA–DNA synaptic and D-loop structures. Nature, 586(7831), 801–806. https://doi.org/10.1038/s41586-020-2820-9<br />
<br />
== UvrD ==<br />
<scene name='92/925553/Uvrd/1'>UvrD</scene>, also known as Helicase II, is one of many components responsible in repairing DNA damage. Helicases use energy from ATP to unwind double helices in metabolic pathways using nucleic acids. ATP molecules are typically used to store energy shared between phosphate groups that gets released when breaking bonds to drive catabolic reactions. <br />
<br />
Helicases were found in the 1970’s to be DNA-dependent ATPases, meaning that they use ATP hydrolysis to complete its interactions with the different types of nucleic acids it comes into contact with. Helicase II, also called UvrD is the founding member of SF1, one group of six superfamiliies used to identify helicases. SF1 and SF2 members share seven conserved sequence motifs that are involved in ATP Binding <ref name="ATP Binding">PMID:17190599</ref>. UvrD is important in replication, recombination, and repair from ultraviolet damage and mismatched base pairs. Nucleotide excision repair in a normal cell is supposed to correct pyrimidine dimers and other DNA lesions when bases are displaced from their normal positions. UvrD pairs up with the UvrABC endonuclease system, which works to displace the DNA. This is then repaired by PolI and DNA ligase <ref>Voet, D., Voet, J., &amp; Pratt, C. (2015). Fundamentals of Biochemistry: Life at the Molecular Level (4th ed.). Wiley</ref>. <br />
<br />
== UvrD Motifs == <br />
There are<scene name='92/925553/Uvrd_labeled_motifs_complete/3'> 16 binding motifs</scene> for UvrD, which are conserved in other homologous structures. The homologous structures mentioned are Helicase 2 homologs, which appear in different species. These conserved motifs are important to maintain the function of UvrD. There are 4 domains that these motifs fit into (not shown). The domains are 1A, 1B, 2A, and 2B. Motifs I, Ia, II-VI are involved in ATP binding. Motifs Ia, III, and V are involved in ssDNA binding. Motif IV is reported to be unique in SF1. They found in their paper, seven new sequence motifs conserved among UvrD homologs. They are Ib, Ic, Id, IVb, IVc, Va, and VIa. These conserved residues are involved in DNA binding or domain 1B and 2B interactions <ref name="ATP_Binding" />.<br />
== Separation Pin ==<br />
The "<scene name='92/925553/Pin_complex/2'>separation pin</scene>" is a part of the 2B domain and is responsible for unwinding the DNA. This uses a 2 step power stroke, one stroke when ATP is bound and another stroke when ADP and P<sub>i</sub> are released. The GIG motif and separation pin work together to unwind the DNA and move it out of the way so UvrD can unwind more DNA. The separation pin also prevents ssDNA once unwound from moving backwards and from reannealing. The proposed method is called the wrench-and-inchworm method, which is when the enzyme binds DNA and attaches at different points and then moves 1 nucleotide per ATP molecule.After an ATP molecule is released, UvrD is then ready to proceed forward to the next nucleotide <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (AMPPNP) ==<br />
When determining the structure of UvrD, an ATP analog was used. They used an <scene name='92/925553/Atp_analog/3'>ATP analog</scene> so that the last phosphate can't be cleaved. Using the unhydrolyzable analog is beneficial in locking in the structure to observe.The green ion shown in the ATP analog scene is a Mg<sup>2+</sup> ion, which is essential for ATP hydrolysis and interacts with the β and γ phosphates. The magnesium ion is surrounded by essential residues that when altered, have been shown to have reduced ATPase activity <ref name="ATP_Binding" />.<br />
== UvrD Binding Site for ATP analog (ADP•MgF<sub>3</sub>) ==<br />
To capture the UvrD-DNA-ADP complex, a new crystal structure used ADP•MgF<sub>3</sub> after NaF was added to help improve crystal growth. This structure is believed to be a more authentic transition state analog, which differs from the AMPPNP analog slightly. The <scene name='92/925553/Adp_analog_complete/1'>ADP analog</scene> has a <scene name='92/925553/Adp_e566_and_gol/2'>GOL region</scene>, which is a glycerol molecule, which has hydrogen bonding similar to interactions that E566 has to a 3' OH of the ribose. The DNA isn't actually bound in the crystal structure, but can be used to visualize what hydrogen bonding might look like when connected to the backbone in DNA. <scene name='92/925553/Adp_e566_and_gol_hbonding_comp/2'>This glycerol molecule hydrogen bonds with E566</scene>, which typically would bind to the 3' OH of the ribose of DNA. Another residue, R37 (Not Shown), binds to the 2' OH of ribose, which has weaker hydrogen bonding. This is a structural component that allows UvrD to bind both ATP and dATP<ref name="ATP_Binding" />. <br />
</StructureSection><br />
<br />
For more structures, please see [[DNA Replication, Repair, and Recombination]]<br />
<br />
==References==<br />
<br />
<references /><br />
<br />
==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644261Sandbox reserved 17532022-10-18T20:16:47Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The<scene name='92/927197/Active_site/7'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644045Sandbox reserved 17532022-10-11T02:43:19Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped the damaged bases out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644044Sandbox reserved 17532022-10-11T02:39:54Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix.ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644043Sandbox reserved 17532022-10-11T02:38:06Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. The dsDNA in the 3D model contains a U G base pair mismatch. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix.ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644042Sandbox reserved 17532022-10-11T02:35:50Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it.The dsDNA has a 10bp that contains a U G base pair mismatch. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix.ASN 204 and HIS 268 are responsible for catalyzing the cleavage of the glycosidic bond. TYR 147, PHE 158, and ASN 204 all aid in Uracil excision and replacement with Thymine. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644039Sandbox reserved 17532022-10-10T20:51:21Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER corrects DNA damage that occurs from oxidation and methylation. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. It also corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it.The dsDNA has a 10bp that contains a U G base pair mismatch. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3644014Sandbox reserved 17532022-10-10T18:17:11Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/5'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643991Sandbox reserved 17532022-10-10T01:02:10Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/2'>Uracil_Glycosylase interaction</scene> and flipping of the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643990Sandbox reserved 17532022-10-10T00:33:13Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/2'>Uracil_Glycosylase interaction</scene>and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643989Sandbox reserved 17532022-10-10T00:21:49Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/4'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643988Sandbox reserved 17532022-10-10T00:17:50Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in RNA. So if a Uracil is found in dsDNA then that means one of the strands has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643987Sandbox reserved 17532022-10-10T00:16:06Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643986Sandbox reserved 17532022-10-10T00:15:31Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643985Sandbox reserved 17532022-10-10T00:15:03Z<p>Casimiro Soliz: </p>
<hr />
<div>==DNA Repair Mechanism; URACIL-DNA GLYCOSYLASE==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643984Sandbox reserved 17532022-10-10T00:13:43Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643983Sandbox reserved 17532022-10-10T00:12:46Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA., Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643982Sandbox reserved 17532022-10-10T00:09:59Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA., Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643981Sandbox reserved 17532022-10-10T00:08:23Z<p>Casimiro Soliz: </p>
<hr />
<div>== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA., Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643980Sandbox reserved 17532022-10-10T00:04:04Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows the <scene name='92/927197/Uracil_glycolysis_interaction/1'>Uracil and Glycosylase interaction</scene> to bind the DNA and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643979Sandbox reserved 17532022-10-09T23:13:46Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix<ref>PMID:25252105</ref>. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase<ref>PMID:9724657</ref>. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows Uracil Glycosylase to bind the DNA and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic<ref>PMID:8900285</ref>. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643978Sandbox reserved 17532022-10-09T23:07:49Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows Uracil Glycosylase to bind the DNA and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
==References==<br />
<ref>PMID:25252105</ref><br />
<ref>PMID:8900285</ref><br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643977Sandbox reserved 17532022-10-09T20:16:34Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows Uracil Glycosylase to bind the DNA and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643976Sandbox reserved 17532022-10-09T20:11:58Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER). Base Excision Repair is a DNA repair mechanism that fixes the most common type of DNA damage. BER removes and repairs damaged bases usually these are single-stranded DNA breaks. BER corrects DNA damage that results from small leisures that do not disrupt the double helix. <br />
<br />
== Function ==<br />
Glycosylase does this by cleaving the glycosidic bond of the damaged nucleotide, leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved by AP endonuclease creating an AP site. The gap that is left is filled in through DNA Polymerase and DNA ligase. <br />
<br />
== Uracil-DNA Glycosylase ==<br />
The structure of Glycosylase has a couple of different forms in terms of its general structure there is Adenine and Uracil Glycosylase. DNA Uracil-Glycosylase specifically looks for any Uracil in the double-stranded DNA. It looks for Uracil in dsDNA because uracil is only found in ssDNA. So if a Uracil is found in dsDNA then that means the strand has been damaged and needs repair. When Uracil-DNA Glycosylase finds the <scene name='92/927197/Uracil/3'>Uracil</scene> site it binds to it. Then a nucleotide-flipping mechanism flips the site of repair out of the double helix. The <scene name='92/927197/Active_site/1'>Active Site</scene> of Uracil Glycosylase; D145, Y147, F158, N204, H268, L272 is what binds to the double-stranded DNA with the damaged lesion. The dsDNA has a 10bp that contains a U G base pair mismatch. This is what allows Uracil Glycosylase to bind the DNA and flip the damaged site out of the double helix. When flipped out of the helix <scene name='92/927197/Arg_side_chain/1'>ARG 272 side chain</scene> takes its place in the minor groove since AP sites can be mutagenic. The Uracil is then replaced with a Thymine. This is because Uracil and Thymine have identical base pairing properties. Thymine happens to have greater resistance to photochemical mutations which is why we see it in dsDNA and not Uracil. <br />
<br />
<br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3643969Sandbox reserved 17532022-10-09T18:11:21Z<p>Casimiro Soliz: </p>
<hr />
<div>==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any <scene name='92/927197/Uracil/3'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER) it removes and repairs damaged bases usually these are single stranded DNA breaks. BER corrects DNA damage that resulted from small leisures that do not disrupt the double helix. The way Glycosylase does this is by first cleaving the glycosidic bond of the damaged nucleotide leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved as well by AP endonuclease. The gap that is left is filled in through DNA Polymerase and DNA ligase. <scene name='92/927197/Active_site/1'>Active Site</scene><br />
The structure of Glycosylase has a couple different forms in terms of its general structure. It is composed of a 10bp DNA that contains U G base pair mismatch. This is what allows it to bind the DNA flipping them out of the double helix. When the uracil mismatch is flipped out of the helix an <scene name='92/927197/Arg_side_chain/1'>ARG side chain</scene> takes its place. The actual structure is composed of a protein section bound to a DNA section. This is often represented by showing the DNA section in stick form and coloring it based on the different atoms bound. The protein section is characterized using a ribbon diagram. In our biochemistry book page 897 there is a representation of this as well. <br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641343Sandbox reserved 17532022-10-04T13:06:00Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]<br />
<br />
<br />
==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any <scene name='92/927197/Uracil/3'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER) it removes and repairs damaged bases usually these are single stranded DNA breaks. BER corrects DNA damage that resulted from small leisures that do not disrupt the double helix. The way Glycosylase does this is by first cleaving the glycosidic bond of the damaged nucleotide leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved as well by AP endonuclease. The gap that is left is filled in through DNA Polymerase and DNA ligase. <scene name='92/927197/Active_site/1'>Active Site</scene><br />
The structure of Glycosylase has a couple different forms in terms of its general structure. It is composed of a 10bp DNA that contains U G base pair mismatch. This is what allows it to bind the DNA flipping them out of the double helix. When the uracil mismatch is flipped out of the helix an <scene name='92/927197/Arg_side_chain/1'>ARG side chain</scene> takes its place. The actual structure is composed of a protein section bound to a DNA section. This is often represented by showing the DNA section in stick form and coloring it based on the different atoms bound. The protein section is characterized using a ribbon diagram. In our biochemistry book page 897 there is a representation of this as well. <br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641342Sandbox reserved 17532022-10-04T12:57:13Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]<br />
<br />
<br />
==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any <scene name='92/927197/Uracil/3'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER) it removes and repairs damaged bases usually these are single stranded DNA breaks. BER corrects DNA damage that resulted from small leisures that do not disrupt the double helix. The way Glycosylase does this is by first cleaving the glycosidic bond of the damaged nucleotide leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved as well by AP endonuclease. The gap that is left is filled in through DNA Polymerase and DNA ligase. <br />
The structure of Glycosylase has a couple different forms in terms of its general structure. It is composed of a 10bp DNA that contains U G base pair mismatch. This is what allows it to bind the DNA flipping them out of the double helix. When the uracil mismatch is flipped out of the helix an <scene name='92/927197/Arg_side_chain/1'>ARG side chain</scene> takes its place. The actual structure is composed of a protein section bound to a DNA section. This is often represented by showing the DNA section in stick form and coloring it based on the different atoms bound. The protein section is characterized using a ribbon diagram. In our biochemistry book page 897 there is a representation of this as well. <br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641292Sandbox reserved 17532022-10-02T22:44:37Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]<br />
<br />
<br />
==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any <scene name='92/927197/Uracil/2'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER) it removes and repairs damaged bases usually these are single stranded DNA breaks. BER corrects DNA damage that resulted from small leisures that do not disrupt the double helix. The way Glycosylase does this is by first cleaving the glycosidic bond of the damaged nucleotide leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved as well by AP endonuclease. The gap that is left is filled in through DNA Polymerase and DNA ligase. <br />
The structure of Glycosylase has a couple different forms in terms of its general structure. It is composed of a 10bp DNA that contains U G base pair mismatch. This is what allows it to bind the DNA flipping them out of the double helix. When the uracil mismatch is flipped out of the helix an <scene name='92/927197/Arg_side_chain/1'>ARG side chain</scene> takes its place. The actual structure is composed of a protein section bound to a DNA section. This is often represented by showing the DNA section in stick form and coloring it based on the different atoms bound. The protein section is characterized using a ribbon diagram. In our biochemistry book page 897 there is a representation of this as well. <br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641291Sandbox reserved 17532022-10-02T22:14:17Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]<br />
<br />
<br />
==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any <scene name='92/927197/Uracil/1'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER) it removes and repairs damaged bases usually these are single stranded DNA breaks. BER corrects DNA damage that resulted from small leisures that do not disrupt the double helix. The way Glycosylase does this is by first cleaving the glycosidic bond of the damaged nucleotide leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved as well by AP endonuclease. The gap that is left is filled in through DNA Polymerase and DNA ligase. <br />
The structure of Glycosylase has a couple different forms in terms of its general structure. It is composed of a 10bp DNA that contains U G base pair mismatch. This is what allows it to bind the DNA flipping them out of the double helix. When the uracil mismatch is flipped out of the helix an <scene name='92/927197/Arg_side_chain/1'>ARG side chain</scene> takes its place. The actual structure is composed of a protein section bound to a DNA section. This is often represented by showing the DNA section in stick form and coloring it based on the different atoms bound. The protein section is characterized using a ribbon diagram. In our biochemistry book page 897 there is a representation of this as well. <br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641290Sandbox reserved 17532022-10-02T22:02:16Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]<br />
<br />
<br />
==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any <scene name='92/927197/Uracil/1'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
== Introduction ==<br />
Glycosylase is an enzyme. Its main function is in Base Excision Repair(BER) it removes and repairs damaged bases usually these are single stranded DNA breaks. BER corrects DNA damage that resulted from small leisures that do not disrupt the double helix. The way Glycosylase does this is by first cleaving the glycosidic bond of the damaged nucleotide leaving the Deoxyribose nucleotide with no base. The deoxyribose is then cleaved as well by AP endonuclease. The gap that is left is filled in through DNA Polymerase and DNA ligase. <br />
The structure of Glycosylase has a couple different forms in terms of its general structure. It is composed of a 10bp DNA that contains U G base pair mismatch. This is what allows it to bind the DNA flipping them out of the double helix. The actual structure is composed of a protein section bound to a DNA section. This is often represented by showing the DNA section in stick form and coloring it based on the different atoms bound. The protein section is characterized using a ribbon diagram. In our biochemistry book page 897 there is a representation of this as well. <br />
<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641289Sandbox reserved 17532022-10-02T21:55:46Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]<br />
<br />
<br />
==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any <scene name='92/927197/Uracil/1'>Uracil</scene> bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641288Sandbox reserved 17532022-10-02T19:18:55Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]<br />
<br />
<br />
==A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA==<br />
<StructureSection load='4skn' size='340' side='right'caption='[[4skn]], [[Resolution|resolution]] 2.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[4skn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SKN FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URA:URACIL'>URA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr><br />
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4skn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4skn OCA], [https://pdbe.org/4skn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4skn RCSB], [https://www.ebi.ac.uk/pdbsum/4skn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4skn ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref> <br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/4skn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4skn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Any uracil bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.<br />
<br />
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.,Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA Nature. 1996 Nov 7;384(6604):87-92. PMID:8900285<ref>PMID:8900285</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 4skn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Human]]<br />
[[Category: Large Structures]]<br />
[[Category: Uridine nucleosidase]]<br />
[[Category: Arvai, A S]]<br />
[[Category: Kavli, B]]<br />
[[Category: Krokan, H E]]<br />
[[Category: Mol, C D]]<br />
[[Category: Slupphaug, G]]<br />
[[Category: Tainer, J A]]<br />
[[Category: Dna]]<br />
[[Category: Dna base excision repair]]<br />
[[Category: Dna glycosylase]]<br />
[[Category: Hydrolase-dna complex]]<br />
[[Category: Uracil]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641287Sandbox reserved 17532022-10-02T17:41:09Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, <scene name='92/927197/Dimer_zn2/1'>Dimer ZN2</scene>-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641286Sandbox reserved 17532022-10-02T17:38:41Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='92/927197/Dimer_metal_binding/1'>Dimer Metal binding</scene> (residues 8-40), an <scene name='92/927197/Dimer_extended_linker/1'>Dimer extended Linker</scene> (41-49), and <br />
an <scene name='92/927197/Dimer_alpha_helicaldimerzation/1'>alpha-helicaldimerization element</scene> (50-64). A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3641285Sandbox reserved 17532022-10-02T17:33:53Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a <scene name='92/927197/Dimer/8'>Dimer</scene> to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3631601Sandbox reserved 17532022-09-19T22:53:51Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer/3'>Text To Be Displayed</scene><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3631600Sandbox reserved 17532022-09-19T22:42:48Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer/2'>Text To Be Displayed</scene><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3631599Sandbox reserved 17532022-09-19T22:36:48Z<p>Casimiro Soliz: </p>
<hr />
<div><scene name='92/927197/Dimer/1'>Text To Be Displayed</scene>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]</div>Casimiro Solizhttps://proteopedia.org/index.php?title=Sandbox_reserved_1753&diff=3631544Sandbox reserved 17532022-09-18T19:08:56Z<p>Casimiro Soliz: New page: ==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX== <StructureSection load='1d66' size='340' side='right'caption='1d66, resolution 2.70&Aring;' scene=''> == ...</p>
<hr />
<div>==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==<br />
<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br><br />
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes. <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d66_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d66 ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.<br />
<br />
DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]<br />
*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Atcc 18824]]<br />
[[Category: Large Structures]]<br />
[[Category: Carey, M]]<br />
[[Category: Harrison, S C]]<br />
[[Category: Marmorstein, R]]<br />
[[Category: Ptashne, M]]<br />
[[Category: Double helix]]<br />
[[Category: Protein-dna complex]]<br />
[[Category: Transcription-dna complex]]</div>Casimiro Soliz