Proteopedia - User contributions [en]

Sandbox Reserved 1063

2018-01-19T12:22:40Z

Geoffrey C. Hoops:

=='''Adhesin Competence Regulator (AdcR)'''==

<StructureSection load='3TGN' size='350' side='right' caption='[http://www.rcsb.org/pdb/explore/explore.do?structureId=3TGN Adhesin Competence Regulator (3TGN)]' scene=''>
===Introduction===
Adhesin Competence Regulator (<scene name='69/694230/Adcr_space_fill/1'>AdcR</scene>) is a transcriptional regulator that controls the activation of over seventy genes within the bacterium [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae''Streptococcus pneumoniae''] <ref name="Sanson">DOI:10.1093/nar/gku1304 </ref> and is a member of the multiple antibiotic resistance regulator (MarR) protein family <ref> PMID: 23428319</ref>. Members of the Mar R protein family conserve a number of features including a general triangular shape, a two fold pseudosymmetric homodimer, and a winged helix-turn-helix pattern [https://en.wikipedia.org/wiki/Helix-turn-helix (wHTH)] which can be seen in Figure 1. AdcR exhibits these conserved features as well, while also exhibiting its own distinct features.

[[Image:MarR_protein_family_slide.png|500px|left|thumb|'''Figure 1: MarR protein family features'''. Proteins MarR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3bpx (3BPX)], HucR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2FBK (2FBK)], TcaR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3KP5 (3KP5)], and OhrR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2pfb (2PFB)] are pictured above with conserved features of the MarR protein family highlighted]]
In contrast with other members of the MarR family, AdcR is metal dependent. Zinc plays a vital role in organism homeostasis, acting as a [https://en.wikipedia.org/wiki/Cofactor_(biochemistry) co-factor] and a regulator of enzymatic activity. However zinc can lead to cell toxicity and deficiency of other vital metals that are also necessary for protein function <ref> DOI: 10.1021/cr900077w</ref>. Binding of Zinc allows AdcR to bind DNA and activate the transcription of high-affinity Zinc specific uptake transporters. The importance of AdcR in ''Streptococcus pneumoniae'' can be understood provided its ability to regulate zinc transfer proteins within the bacteria.

==='''Structural Overview'''===
[[Image:Screen Shot 2017-04-18 at 11.56.32 PM.png|300 px|right|thumb|'''Figure 2'''. A generic protein representing the [https://images.google.com/imgres?imgurl=https%3A%2F%2Fclassconnection.s3.amazonaws.com%2F838%2Fflashcards%2F2220838%2Fjpg%2Fasdf-144940F88BA53A918F3.jpg&imgrefurl=https%3A%2F%2Fwww.studyblue.com%2Fnotes%2Fnote%2Fn%2Flecture-13%2Fdeck%2F10226974&docid=qBvv1vgKeLTGcM&tbnid=3nuaRjPWKUBfqM%3A&vet=1&w=741&h=756&hl=en&source=sh%2Fx%2Fim wHTH] motif binding the major and minor groove of DNA similar to AdcR.]]
One of the two functional domains of AdcR is the <scene name='69/694230/Dimerization_domain/3'> dimerization domain</scene>. This domain connects and stabilizes the two pseudosymmetric protomers and is composed of the <scene name='69/694230/Alpha_1/1'>α1 helix</scene>, the <scene name='69/694230/Alpha_6/1'>α6 helix</scene> . and the C-terminus of the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> . This domain is connected to the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain] by the long α5 helix. The DNA binding domain interacts with the major and minor grooves of DNA via the <scene name='69/694230/Whth_4/7'>winged helix-turn-helix (wHTH)</scene> motif (Figure 2). The binding of Zinc to the <scene name='69/694230/2_binding_sites/4'>Zinc binding pocket</scene> induces a conformational change that allows for a <scene name='69/694230/Hydrogen_bonding_1/4'>hydrogen bond network</scene> between 4 specific residues. This network connects multiple helices from the metal binding pockets and DNA binding domain, and is believed play a critical role in the allosteric activation of AdcR, allowing the protein to bind exposed bases along the major and minor grooves of the DNA ligand <ref name="guerra">PMID:22085181</ref>. Thus, the protein is able to perform its biological function by activating transcription after binding DNA.

== '''DNA Binding''' ==
=== Helix-Turn-Helix Motif ===
[[Image:Charge_map.jpg |300 px|right|thumb|'''Figure 3'''. A charge map of AdcR shows the general triangular shape and the positively charged area on the tips of the wHTH motif]]
The AdcR MarR transcriptional regulator's structure resembles that of other proteins in the MarR family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA <ref name="guerra" />. The <scene name='69/694230/Whth_4/7'>winged helix turn helix</scene> motif is made up of the α3 and α4 helices along with <scene name='69/694230/Anti-parallel_beta_sheet/2'>anti-parallel β sheets</scene> on each side. There is one wHTH motif per monomer. The recognition helix, or the α4 helix, binds the major groove of DNA through [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions] between exposed bases <ref name="guerra" />. The wings of the helix bind the minor groove of DNA while the other helices stabilize the DNA and Protein upon binding. The two anti parallel β sheets contain several <scene name='69/694230/Positive_residues_on_wing_3/4'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA. The charge map (Figure 3) highlights the dark blue tips of the wHTH motif consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. The residues are only shown on the random loop of one monomer because the random loop on the other protein monomer <scene name='69/694230/Uncrystallized_loop/1'>was not crystallized</scene>.

== '''Zn(II) Binding''' ==
Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/2_binding_sites/4'>two binding sites for zinc</scene> on each of its two protomers and can bind a total of four Zn(II) ions. The <scene name='69/694230/Alpha1-alpha2_loop/2'>α1-α2 loop</scene> combined with the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> and <scene name='69/694230/Alpha_2/1'>α2 helix</scene> contribute residues to the <scene name='69/694230/Two_binding_sites/2'>metal binding sites</scene>. Each protomer has one high affinity site (Binding site 1; KZn1 = 1012 M; pH 8) and one low affinity binding site (Binding Site 2; KZn2 = 107 M; pH 8) <ref name="Reyes">PMID:20804771</ref>. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/5'>hydrogen bonding</scene> of H108 and E41.
=== Binding Site 1 ===
<scene name='69/694230/Binding_site_1/5'>Binding site 1</scene> consists of a distorted tetrahedral geometry around Zn(II). The four amino acids involved in zinc binding are E24, H42, H108, and H112. Binding site 1 is the only binding site that plays a significant role in the protein's regulatory function. The ability of binding site 1 to coordinate to the Zn(II) ion is pH dependent. At pH 6 the binding affinity for the Zn(II) ion is 109 - 1010 M-1, but at pH 8 the binding affinity increases to 1012 M-1 <ref name="Reyes" />. This is due to the charges on the histidines of the binding site. At pH 6, the histidines are positively charged and are not able to interact with the positively charged Zn(II) ion. However, at pH 8 the histidines are neutrally charged and are able to coordinate with Zn(II), which increases the overall binding affinity. The AdcR MarR transcriptional regulator is able to bind Co(II) in binding site 1 in a way that induces similar conformational changes to Zn(II) binding. Co(II) coordination in binding site 1 is able to allosterically activate DNA binding similarly to Zn(II) binding <ref name="guerra" />.

=== Binding Site 2 ===
<scene name='69/694230/Binding_site_2/4'>Binding site 2</scene> consists of a highly distorted tetrahedral geometry around the zinc ion. There are three amino acids involved in the binding of the zinc ion (C30, E41, and E107) as well as a water molecule (shown as a red sphere). When Cys30 in binding site 2 is mutated to an alanine, it has no effect on the ability of the protein to bind DNA <ref name="guerra" />. Therefore, binding site 2 has no significant role in the ability of AdcR to bind to DNA and AdcR is still able to function with no zinc bound present in binding site 2. In fact, the presence of binding site 2 may simply be due to an excess of zinc during the crystallization process.

=== Hydrogen Bond Network ===
[[Image:H Bonding of DNA.png|300 px|left|thumb|'''Figure 4'''. The Hydrogen Bonding Network is shown with dotted green lines approximately 2.8 angstroms between residues.]]
The binding of zinc metals creates a hydrogen bond network (Figure 4) within the protein that connects the metal binding sites and the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain]. The <scene name='69/694230/Hydrogen_bonding_1/5'>hydrogen bond network</scene> (<scene name='69/694230/Hydrogen_bonding_2/5'>with measurements</scene>) (residues in stick structures, colored by atom type) is characteristic of the MarR family as a whole and connects the metal binding pockets to the α4 helix also known as the DNA recognition helix. <scene name='69/694230/Recognition_helix/3'>Several residues</scene> in this helix recognize the DNA ligand. The hydrogen bond network connects the α2 and α4 helices via hydrogen bonding between specific residues. After zinc is bound, a glutamate (E24) residue from a random coil accepts a hydrogen bond from the carboxamide end of an asparagine (N38) residue from the α2 helix. A glutamine (Q40) residue from α2 helix accepts a hydrogen bond from a serine (S74) residue from the α4 helix <ref name="guerra" />.

== '''Clinical Relevance''' ==
''Streptococcus pneumoniae'' is a significant pathogenic bacterium. Although asymptomatic in healthy individuals, ''S. pneumoniae'' can lead to Bronchitis, meningitis conjunctivitis, or brain abscesses in those with weaker immune systems. Host regulation of zinc is often used to combat pathogens such as ''S. pneumoniae'' <ref name="Sanson" />. A better understanding of AdcR, the regulator that controls the transcription of zinc specific uptake transporters, could help to illuminate better mechanism for combating not only ''S. pneumoniae'', but other comparable bacteria.

</StructureSection>

== References ==
<references/>

Sandbox Reserved 1063

2018-01-19T12:20:50Z

Geoffrey C. Hoops:

=='''Adhesin Competence Regulator (AdcR)'''==

<StructureSection load='3TGN' size='350' side='right' caption='[http://www.rcsb.org/pdb/explore/explore.do?structureId=3TGN Adhesin Competence Regulator (3TGN)]' scene=''>
===Introduction===
Adhesin Competence Regulator (<scene name='69/694230/Adcr_space_fill/1'>AdcR</scene>) is a transcriptional regulator that controls the activation of over seventy genes within the bacterium [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae''Streptococcus pneumoniae''] <ref name="Sanson">DOI:10.1093/nar/gku1304 </ref> and is a member of the multiple antibiotic resistance regulator (MarR) protein family <ref> PMID: 23428319</ref>. Members of the Mar R protein family conserve a number of features including a general triangular shape, a two fold pseudosymmetric homodimer, and a winged helix-turn-helix pattern [https://en.wikipedia.org/wiki/Helix-turn-helix (wHTH)] which can be seen in Figure 1. AdcR exhibits these conserved features as well, while also exhibiting its own distinct features.

[[Image:MarR_protein_family_slide.png|500px|left|thumb|'''Figure 1'''. Proteins MarR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3bpx (3BPX)], HucR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2FBK (2FBK)], TcaR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3KP5 (3KP5)], and OhrR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2pfb (2PFB)] are pictured above with conserved features of the MarR protein family highlighted]]
In contrast with other members of the MarR family, AdcR is metal dependent. Zinc plays a vital role in organism homeostasis, acting as a [https://en.wikipedia.org/wiki/Cofactor_(biochemistry) co-factor] and a regulator of enzymatic activity. However zinc can lead to cell toxicity and deficiency of other vital metals that are also necessary for protein function <ref> DOI: 10.1021/cr900077w</ref>. Binding of Zinc allows AdcR to bind DNA and activate the transcription of high-affinity Zinc specific uptake transporters. The importance of AdcR in ''Streptococcus pneumoniae'' can be understood provided its ability to regulate zinc transfer proteins within the bacteria.

==='''Structural Overview'''===
[[Image:Screen Shot 2017-04-18 at 11.56.32 PM.png|300 px|right|thumb|'''Figure 2'''. A generic protein representing the [https://images.google.com/imgres?imgurl=https%3A%2F%2Fclassconnection.s3.amazonaws.com%2F838%2Fflashcards%2F2220838%2Fjpg%2Fasdf-144940F88BA53A918F3.jpg&imgrefurl=https%3A%2F%2Fwww.studyblue.com%2Fnotes%2Fnote%2Fn%2Flecture-13%2Fdeck%2F10226974&docid=qBvv1vgKeLTGcM&tbnid=3nuaRjPWKUBfqM%3A&vet=1&w=741&h=756&hl=en&source=sh%2Fx%2Fim wHTH] motif binding the major and minor groove of DNA similar to AdcR.]]
One of the two functional domains of AdcR is the <scene name='69/694230/Dimerization_domain/3'> dimerization domain</scene>. This domain connects and stabilizes the two pseudosymmetric protomers and is composed of the <scene name='69/694230/Alpha_1/1'>α1 helix</scene>, the <scene name='69/694230/Alpha_6/1'>α6 helix</scene> . and the C-terminus of the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> . This domain is connected to the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain] by the long α5 helix. The DNA binding domain interacts with the major and minor grooves of DNA via the <scene name='69/694230/Whth_4/7'>winged helix-turn-helix (wHTH)</scene> motif (Figure 2). The binding of Zinc to the <scene name='69/694230/2_binding_sites/4'>Zinc binding pocket</scene> induces a conformational change that allows for a <scene name='69/694230/Hydrogen_bonding_1/4'>hydrogen bond network</scene> between 4 specific residues. This network connects multiple helices from the metal binding pockets and DNA binding domain, and is believed play a critical role in the allosteric activation of AdcR, allowing the protein to bind exposed bases along the major and minor grooves of the DNA ligand <ref name="guerra">PMID:22085181</ref>. Thus, the protein is able to perform its biological function by activating transcription after binding DNA.

== '''DNA Binding''' ==
=== Helix-Turn-Helix Motif ===
[[Image:Charge_map.jpg |300 px|right|thumb|'''Figure 3'''. A charge map of AdcR shows the general triangular shape and the positively charged area on the tips of the wHTH motif]]
The AdcR MarR transcriptional regulator's structure resembles that of other proteins in the MarR family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA <ref name="guerra" />. The <scene name='69/694230/Whth_4/7'>winged helix turn helix</scene> motif is made up of the α3 and α4 helices along with <scene name='69/694230/Anti-parallel_beta_sheet/2'>anti-parallel β sheets</scene> on each side. There is one wHTH motif per monomer. The recognition helix, or the α4 helix, binds the major groove of DNA through [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions] between exposed bases <ref name="guerra" />. The wings of the helix bind the minor groove of DNA while the other helices stabilize the DNA and Protein upon binding. The two anti parallel β sheets contain several <scene name='69/694230/Positive_residues_on_wing_3/4'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA. The charge map (Figure 3) highlights the dark blue tips of the wHTH motif consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. The residues are only shown on the random loop of one monomer because the random loop on the other protein monomer <scene name='69/694230/Uncrystallized_loop/1'>was not crystallized</scene>.

== '''Zn(II) Binding''' ==
Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/2_binding_sites/4'>two binding sites for zinc</scene> on each of its two protomers and can bind a total of four Zn(II) ions. The <scene name='69/694230/Alpha1-alpha2_loop/2'>α1-α2 loop</scene> combined with the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> and <scene name='69/694230/Alpha_2/1'>α2 helix</scene> contribute residues to the <scene name='69/694230/Two_binding_sites/2'>metal binding sites</scene>. Each protomer has one high affinity site (Binding site 1; KZn1 = 1012 M; pH 8) and one low affinity binding site (Binding Site 2; KZn2 = 107 M; pH 8) <ref name="Reyes">PMID:20804771</ref>. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/5'>hydrogen bonding</scene> of H108 and E41.
=== Binding Site 1 ===
<scene name='69/694230/Binding_site_1/5'>Binding site 1</scene> consists of a distorted tetrahedral geometry around Zn(II). The four amino acids involved in zinc binding are E24, H42, H108, and H112. Binding site 1 is the only binding site that plays a significant role in the protein's regulatory function. The ability of binding site 1 to coordinate to the Zn(II) ion is pH dependent. At pH 6 the binding affinity for the Zn(II) ion is 109 - 1010 M-1, but at pH 8 the binding affinity increases to 1012 M-1 <ref name="Reyes" />. This is due to the charges on the histidines of the binding site. At pH 6, the histidines are positively charged and are not able to interact with the positively charged Zn(II) ion. However, at pH 8 the histidines are neutrally charged and are able to coordinate with Zn(II), which increases the overall binding affinity. The AdcR MarR transcriptional regulator is able to bind Co(II) in binding site 1 in a way that induces similar conformational changes to Zn(II) binding. Co(II) coordination in binding site 1 is able to allosterically activate DNA binding similarly to Zn(II) binding <ref name="guerra" />.

=== Binding Site 2 ===
<scene name='69/694230/Binding_site_2/4'>Binding site 2</scene> consists of a highly distorted tetrahedral geometry around the zinc ion. There are three amino acids involved in the binding of the zinc ion (C30, E41, and E107) as well as a water molecule (shown as a red sphere). When Cys30 in binding site 2 is mutated to an alanine, it has no effect on the ability of the protein to bind DNA <ref name="guerra" />. Therefore, binding site 2 has no significant role in the ability of AdcR to bind to DNA and AdcR is still able to function with no zinc bound present in binding site 2. In fact, the presence of binding site 2 may simply be due to an excess of zinc during the crystallization process.

=== Hydrogen Bond Network ===
[[Image:H Bonding of DNA.png|300 px|left|thumb|'''Figure 4'''. The Hydrogen Bonding Network is shown with dotted green lines approximately 2.8 angstroms between residues.]]
The binding of zinc metals creates a hydrogen bond network (Figure 4) within the protein that connects the metal binding sites and the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain]. The <scene name='69/694230/Hydrogen_bonding_1/5'>hydrogen bond network</scene> (<scene name='69/694230/Hydrogen_bonding_2/5'>with measurements</scene>) (residues in stick structures, colored by atom type) is characteristic of the MarR family as a whole and connects the metal binding pockets to the α4 helix also known as the DNA recognition helix. <scene name='69/694230/Recognition_helix/3'>Several residues</scene> in this helix recognize the DNA ligand. The hydrogen bond network connects the α2 and α4 helices via hydrogen bonding between specific residues. After zinc is bound, a glutamate (E24) residue from a random coil accepts a hydrogen bond from the carboxamide end of an asparagine (N38) residue from the α2 helix. A glutamine (Q40) residue from α2 helix accepts a hydrogen bond from a serine (S74) residue from the α4 helix <ref name="guerra" />.

== '''Clinical Relevance''' ==
''Streptococcus pneumoniae'' is a significant pathogenic bacterium. Although asymptomatic in healthy individuals, ''S. pneumoniae'' can lead to Bronchitis, meningitis conjunctivitis, or brain abscesses in those with weaker immune systems. Host regulation of zinc is often used to combat pathogens such as ''S. pneumoniae'' <ref name="Sanson" />. A better understanding of AdcR, the regulator that controls the transcription of zinc specific uptake transporters, could help to illuminate better mechanism for combating not only ''S. pneumoniae'', but other comparable bacteria.

</StructureSection>

== References ==
<references/>

CzrA

2018-01-19T01:47:47Z

Geoffrey C. Hoops:

<StructureSection load='CzrAwithDNA.pdb' size='340' frame='true' side='right' caption='The dimer Czr A' scene=''>
<scene name='69/694220/Czra_with_dna/1'>CzrA</scene> is a transcriptional repressor protein responsible for the regulation of the Czr operon in prokaryotes. The best studied example to date comes from ''Staphylococcus aureus''.
==Biological Function==
===Operon Overview===
[https://en.wikipedia.org/wiki/Operon Operons] are a critical genetic component of most prokaryotic cells. There are many different operons, responsible for the production of proteins with a wide range of functions. The most well-known and studied operons are the [https://en.wikipedia.org/wiki/Lac_operon Lac] and [https://en.wikipedia.org/wiki/Trp_operon Trp] operons, responsible for producing enzymes which metabolize lactose and tryptophan respectively. Despite many differences in each operon and the proteins that they encode, operons all function in the same general manner (Figure 1). Each operon contains a [https://en.wikipedia.org/wiki/Regulator_gene regulator], an [https://en.wikipedia.org/wiki/Operator_(biology) operator], and one or more [https://en.wikipedia.org/wiki/Structural_gene structural genes]. The regulator gene codes for a protein responsible for managing the expression level of the structural genes. The operator contains the binding sequence for [https://en.wikipedia.org/wiki/RNA_polymerase RNA polymerase] and is the site where [https://en.wikipedia.org/wiki/Transcription_(biology) transcription] begins. Lastly, the structural genes code for proteins to be used elsewhere. The regulator protein (produced as a result of expression of the regulator gene) usually acts in a repressive manner. The regulator protein will bind to the operator gene, inhibiting the binding and/or progression of RNA polymerase to the structural genes, thus inhibiting transcription of the genes into mRNA. If the regulator protein were always active, the structural genes would never be expressed, so there must be a way to inactive the regulator protein, thus enabling expression of the structural genes. This is usually achieved through the binding of an inhibitor to the regulator protein. Since regulator proteins are DNA binding proteins, often this inhibition is [https://en.wikipedia.org/wiki/Allosteric_regulation allosteric] rather than competitive. The inhibitor of the regulator protein binds to somewhere other than the active site of the protein, changing the conformation of the regulator protein to decrease its ability to bind DNA and repress transcription.
[[Image:Operon.png|500px|thumb|center|Figure 1: Overview of CzrA operon structure]]
===The Czr Operon===
The Chromosome determined zinc responsible (Czr) operon acts as described above (Figure 1), with CzrA acting as a regulator protein to the downstream structural gene CzrB<ref name="critical">Arunkumar A., Campanello G., Giedroc D. (2009). Solution Structure of a
paradigm ArsR family zinc sensor in the DNA-bound state. PNAS 106:43
18177-18182.</ref>. The CzrB gene in turn codes for a Zn+2 pump, the [http://proteopedia.org/wiki/index.php/3byr CzrB] protein. When relatively low amounts of zinc are present in the cell CzrA will bind to the operator on the Czr operon, preventing the progression of RNA polymerase and thus inhibiting expression of CzrB. Decreased expression of CzrB results in a buildup of Zn+2 inside the cell, as there are fewer pumps to export Zn+2. This metal sensing system serves to maintain an appropriate intracellular concentration of Zn+2.
==Structural Overview==
Czr A functions as a [https://en.wikipedia.org/wiki/Protein_dimer dimer] to repress gene transcription. Each <scene name='69/694218/Monomeric_unit/1'>monomeric unit</scene> contains <scene name='69/694218/Helices/1'>five alpha helices</scene> seen in purple and <scene name='69/694218/B_sheets/1'>one antiparallel beta sheet</scene> displayed in yellow. Key [https://en.wikipedia.org/wiki/Alpha_helix helices] regulate the binding of DNA versus Zn+2. The <scene name='69/694220/2kjb_colored_alpha_4/1'>α4 helices</scene> (green) are the location of DNA binding and the <scene name='69/694220/Zinc_pocket_with_residues/2'>α5 helices</scene> (red) contain the Zn+2 binding sites.
==Allosteric Inhibition by Zn+2==
CzrA is allosterically inhibited by the binding of two Zn+2 ions. The structure of CzrA has been determined in two different conformations<ref name="critical"/>; the first has a high affinity for DNA and has no Zn+2 ions bound to it (PDB code: 2KJB). In this conformation the <scene name='69/694220/A5_helices__dna_binding/2'>alpha 5 helices are aligned</scene>. Binding of zinc drives a conformational change (PDB code: 2KJC) in which the <scene name='69/694220/A5_helices_dna_binding/2'>alpha 5 helices become unaligned</scene>, changing the overall shape of the protein and significantly lowering its affinity for DNA (Figure 2). Unfortunately, zinc ions are not directly visible in the 2KJC structure, which was determined by NMR spectroscopy.
[[Image:800px-2KJB + 2KJC side by side.fw.png CROPPED.fw.png|600px|center|thumb| Figure 2: Comparison of Czr A bound to DNA to Czr A with Zn+2 bound. α5 helices are shown in red and the α4 helices shown in green.]]
== DNA Binding Site==
Ser54, Ser57, and His58 are the primary residues involved in <scene name='69/694220/2kjb_colored/3'>DNA interaction</scene> with Czr A<ref name="critical"/>. These residues are likely to interact with the 5'-TGAA sequence found in the half-site of the DNA, where the α4 helices (green) <scene name='69/694219/Czra_with_dna/2'>form an interaction with DNA</scene> (Figure 3). Binding of two Zn+2 ions <scene name='69/694220/Dna_residues_when_inhibited/2'>pushes these residues out of their DNA binding conformation</scene>. Additionally, Val42 and Gln53 (lime green) are involved in the <scene name='69/694220/Val_42_and_gln_53/1'>DNA binding pocket</scene>.

The <scene name='69/694220/Dna_binding_residues/2'>residues directly involved in binding to DNA</scene> Gln53 and Val42 (aqua) as well as the Ser54, Ser57, and His58 (lime) have been individually mutated to Ala, and DNA binding experiments were performed<ref name="critical"/>. Compared to wild type Czr A, Gln53Ala and Val42Ala variants displayed an 11-fold and 160-fold decrease in Ka, respectively. Mutations to the main DNA interaction sites Ser54, Ser57, and His58 result in drastic loss of binding similar to the inhibited non-DNA binding conformational state, suggesting that these residues are essential to binding DNA. While the conformational change that occurs from the Zinc bound state to the DNA bound state is small,the α4 helices (shown in green in Figure 2) are slightly shifted. The loss of DNA binding in the mutagenesis experiments in combination with the lack of any other major physical changes between these two states further suggests that the α4 helices are the location of DNA binding in Czr A. A <scene name='69/694220/Czra_with_dna/1'>computational model of CzrA with DNA bound</scene> (not available in the PDB) has been since been published<ref>PMID:22007899</ref> (Figure 3).

[[Image:800px-DNABound Final.fw.png CROPPED.fw.png|750px|thumb|center| Figure 3: Two views of Czr A bound to DNA. A segment of DNA is shown in orange with the α5 helices displayed in red and the α4 helices shown in green.]]

== Zinc Binding Site==
Many zinc-dependent proteins are transcriptional regulators<ref>DOI: 10.1128/MMBR.00015-06</ref>. Czr A fits into this category as an [https://en.wikipedia.org/wiki/Allosteric_regulation allosteric inhibitor] of the czr operon. Two [https://en.wikipedia.org/wiki/Zinc Zn +2] ions may bind to the dimer<ref name="critical"/>, at the location of the <scene name='69/694220/A5_helices__zn_binding/2'>α5 helix</scene> from each monomer. As zinc binds, the α5 helices <scene name='69/694218/2kjc_zinc_bound/1'>unalign</scene> to inhibit the DNA binding residues (Figure 2). Furthermore, CzrA must be in its dimer form for zinc to bind. The <scene name='69/694220/Spacefill_zinc_pockets/1'>zinc binding pockets</scene> are formed by two residues from each monomer, so Zn+2 cannot bind to the monomer. The <scene name='69/694220/Zinc_binding_residues/7'>zinc binding site</scene> is formed by Asp84 and His 86 from one monomer, as well as His97 and His100 from the other monomer. Zinc ions were not present in the solution NMR structure<ref name="critical"/>, so a representation of a zinc ion in the binding pocket has been drawn in Figure 4. The large number of histidines used in the Czr A zinc pocket is a repetitive and commonly found feature in zinc-binding proteins <ref>Miller J, McLachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun 4;4(6):1609-1614.</ref>.

[[Image:Zinc tetrahedral complex.PNG|350px|thumb|center| Figure 4: Zn+2 tetrahedral binding complex]]

Zn+2 binding is driven by a large [https://en.wikipedia.org/wiki/Entropy entropic] gain <ref>DOI:10.1021/ja906131b</ref>. Water molecules around the metal ion and Czr A protein are displaced, and gain greater freedom. This gain in entropy allows Zn+2 to bind to Czr A with reasonable affinity and speed in vivo. The zinc+2 ion forms a tetrahedral complex with the four residues (Figure 4). Other metal ions that may form a tetrahedral complex will have some affinity for Czr A; however, the metal binding pocket of Czr A has been optimized to bind Zn+2 with the highest affinity.
</StructureSection>

__NOTOC__

== References ==
<references/>

==Student Contributors==
*Katelyn Baumer
*Jakob Jozwiakowski
*Catie Liggett

CzrA

2018-01-19T01:47:10Z

Geoffrey C. Hoops: New page: =Zinc Dependent Transcriptional Repressor of the Czr operon (CzrA)= <StructureSection load='CzrAwithDNA.pdb' size='340' frame='true' side='right' caption='The dimer Czr A' scene=''> <scene...

=Zinc Dependent Transcriptional Repressor of the Czr operon (CzrA)=
<StructureSection load='CzrAwithDNA.pdb' size='340' frame='true' side='right' caption='The dimer Czr A' scene=''>
<scene name='69/694220/Czra_with_dna/1'>CzrA</scene> is a transcriptional repressor protein responsible for the regulation of the Czr operon in prokaryotes. The best studied example to date comes from ''Staphylococcus aureus''.
==Biological Function==
===Operon Overview===
[https://en.wikipedia.org/wiki/Operon Operons] are a critical genetic component of most prokaryotic cells. There are many different operons, responsible for the production of proteins with a wide range of functions. The most well-known and studied operons are the [https://en.wikipedia.org/wiki/Lac_operon Lac] and [https://en.wikipedia.org/wiki/Trp_operon Trp] operons, responsible for producing enzymes which metabolize lactose and tryptophan respectively. Despite many differences in each operon and the proteins that they encode, operons all function in the same general manner (Figure 1). Each operon contains a [https://en.wikipedia.org/wiki/Regulator_gene regulator], an [https://en.wikipedia.org/wiki/Operator_(biology) operator], and one or more [https://en.wikipedia.org/wiki/Structural_gene structural genes]. The regulator gene codes for a protein responsible for managing the expression level of the structural genes. The operator contains the binding sequence for [https://en.wikipedia.org/wiki/RNA_polymerase RNA polymerase] and is the site where [https://en.wikipedia.org/wiki/Transcription_(biology) transcription] begins. Lastly, the structural genes code for proteins to be used elsewhere. The regulator protein (produced as a result of expression of the regulator gene) usually acts in a repressive manner. The regulator protein will bind to the operator gene, inhibiting the binding and/or progression of RNA polymerase to the structural genes, thus inhibiting transcription of the genes into mRNA. If the regulator protein were always active, the structural genes would never be expressed, so there must be a way to inactive the regulator protein, thus enabling expression of the structural genes. This is usually achieved through the binding of an inhibitor to the regulator protein. Since regulator proteins are DNA binding proteins, often this inhibition is [https://en.wikipedia.org/wiki/Allosteric_regulation allosteric] rather than competitive. The inhibitor of the regulator protein binds to somewhere other than the active site of the protein, changing the conformation of the regulator protein to decrease its ability to bind DNA and repress transcription.
[[Image:Operon.png|500px|thumb|center|Figure 1: Overview of CzrA operon structure]]
===The Czr Operon===
The Chromosome determined zinc responsible (Czr) operon acts as described above (Figure 1), with CzrA acting as a regulator protein to the downstream structural gene CzrB<ref name="critical">Arunkumar A., Campanello G., Giedroc D. (2009). Solution Structure of a
paradigm ArsR family zinc sensor in the DNA-bound state. PNAS 106:43
18177-18182.</ref>. The CzrB gene in turn codes for a Zn+2 pump, the [http://proteopedia.org/wiki/index.php/3byr CzrB] protein. When relatively low amounts of zinc are present in the cell CzrA will bind to the operator on the Czr operon, preventing the progression of RNA polymerase and thus inhibiting expression of CzrB. Decreased expression of CzrB results in a buildup of Zn+2 inside the cell, as there are fewer pumps to export Zn+2. This metal sensing system serves to maintain an appropriate intracellular concentration of Zn+2.
==Structural Overview==
Czr A functions as a [https://en.wikipedia.org/wiki/Protein_dimer dimer] to repress gene transcription. Each <scene name='69/694218/Monomeric_unit/1'>monomeric unit</scene> contains <scene name='69/694218/Helices/1'>five alpha helices</scene> seen in purple and <scene name='69/694218/B_sheets/1'>one antiparallel beta sheet</scene> displayed in yellow. Key [https://en.wikipedia.org/wiki/Alpha_helix helices] regulate the binding of DNA versus Zn+2. The <scene name='69/694220/2kjb_colored_alpha_4/1'>α4 helices</scene> (green) are the location of DNA binding and the <scene name='69/694220/Zinc_pocket_with_residues/2'>α5 helices</scene> (red) contain the Zn+2 binding sites.
==Allosteric Inhibition by Zn+2==
CzrA is allosterically inhibited by the binding of two Zn+2 ions. The structure of CzrA has been determined in two different conformations<ref name="critical"/>; the first has a high affinity for DNA and has no Zn+2 ions bound to it (PDB code: 2KJB). In this conformation the <scene name='69/694220/A5_helices__dna_binding/2'>alpha 5 helices are aligned</scene>. Binding of zinc drives a conformational change (PDB code: 2KJC) in which the <scene name='69/694220/A5_helices_dna_binding/2'>alpha 5 helices become unaligned</scene>, changing the overall shape of the protein and significantly lowering its affinity for DNA (Figure 2). Unfortunately, zinc ions are not directly visible in the 2KJC structure, which was determined by NMR spectroscopy.
[[Image:800px-2KJB + 2KJC side by side.fw.png CROPPED.fw.png|600px|center|thumb| Figure 2: Comparison of Czr A bound to DNA to Czr A with Zn+2 bound. α5 helices are shown in red and the α4 helices shown in green.]]
== DNA Binding Site==
Ser54, Ser57, and His58 are the primary residues involved in <scene name='69/694220/2kjb_colored/3'>DNA interaction</scene> with Czr A<ref name="critical"/>. These residues are likely to interact with the 5'-TGAA sequence found in the half-site of the DNA, where the α4 helices (green) <scene name='69/694219/Czra_with_dna/2'>form an interaction with DNA</scene> (Figure 3). Binding of two Zn+2 ions <scene name='69/694220/Dna_residues_when_inhibited/2'>pushes these residues out of their DNA binding conformation</scene>. Additionally, Val42 and Gln53 (lime green) are involved in the <scene name='69/694220/Val_42_and_gln_53/1'>DNA binding pocket</scene>.

The <scene name='69/694220/Dna_binding_residues/2'>residues directly involved in binding to DNA</scene> Gln53 and Val42 (aqua) as well as the Ser54, Ser57, and His58 (lime) have been individually mutated to Ala, and DNA binding experiments were performed<ref name="critical"/>. Compared to wild type Czr A, Gln53Ala and Val42Ala variants displayed an 11-fold and 160-fold decrease in Ka, respectively. Mutations to the main DNA interaction sites Ser54, Ser57, and His58 result in drastic loss of binding similar to the inhibited non-DNA binding conformational state, suggesting that these residues are essential to binding DNA. While the conformational change that occurs from the Zinc bound state to the DNA bound state is small,the α4 helices (shown in green in Figure 2) are slightly shifted. The loss of DNA binding in the mutagenesis experiments in combination with the lack of any other major physical changes between these two states further suggests that the α4 helices are the location of DNA binding in Czr A. A <scene name='69/694220/Czra_with_dna/1'>computational model of CzrA with DNA bound</scene> (not available in the PDB) has been since been published<ref>PMID:22007899</ref> (Figure 3).

[[Image:800px-DNABound Final.fw.png CROPPED.fw.png|750px|thumb|center| Figure 3: Two views of Czr A bound to DNA. A segment of DNA is shown in orange with the α5 helices displayed in red and the α4 helices shown in green.]]

== Zinc Binding Site==
Many zinc-dependent proteins are transcriptional regulators<ref>DOI: 10.1128/MMBR.00015-06</ref>. Czr A fits into this category as an [https://en.wikipedia.org/wiki/Allosteric_regulation allosteric inhibitor] of the czr operon. Two [https://en.wikipedia.org/wiki/Zinc Zn +2] ions may bind to the dimer<ref name="critical"/>, at the location of the <scene name='69/694220/A5_helices__zn_binding/2'>α5 helix</scene> from each monomer. As zinc binds, the α5 helices <scene name='69/694218/2kjc_zinc_bound/1'>unalign</scene> to inhibit the DNA binding residues (Figure 2). Furthermore, CzrA must be in its dimer form for zinc to bind. The <scene name='69/694220/Spacefill_zinc_pockets/1'>zinc binding pockets</scene> are formed by two residues from each monomer, so Zn+2 cannot bind to the monomer. The <scene name='69/694220/Zinc_binding_residues/7'>zinc binding site</scene> is formed by Asp84 and His 86 from one monomer, as well as His97 and His100 from the other monomer. Zinc ions were not present in the solution NMR structure<ref name="critical"/>, so a representation of a zinc ion in the binding pocket has been drawn in Figure 4. The large number of histidines used in the Czr A zinc pocket is a repetitive and commonly found feature in zinc-binding proteins <ref>Miller J, McLachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun 4;4(6):1609-1614.</ref>.

[[Image:Zinc tetrahedral complex.PNG|350px|thumb|center| Figure 4: Zn+2 tetrahedral binding complex]]

Zn+2 binding is driven by a large [https://en.wikipedia.org/wiki/Entropy entropic] gain <ref>DOI:10.1021/ja906131b</ref>. Water molecules around the metal ion and Czr A protein are displaced, and gain greater freedom. This gain in entropy allows Zn+2 to bind to Czr A with reasonable affinity and speed in vivo. The zinc+2 ion forms a tetrahedral complex with the four residues (Figure 4). Other metal ions that may form a tetrahedral complex will have some affinity for Czr A; however, the metal binding pocket of Czr A has been optimized to bind Zn+2 with the highest affinity.
</StructureSection>

__NOTOC__

== References ==
<references/>

==Student Contributors==
*Katelyn Baumer
*Jakob Jozwiakowski
*Catie Liggett

2017-12-04T19:13:35Z

Geoffrey C. Hoops:

=='''Adhesin Competence Regulator'''==

<StructureSection load='3TGN' size='350' side='right' caption='[http://www.rcsb.org/pdb/explore/explore.do?structureId=3TGN Adhesin Competence Regulator (3TGN)]' scene=''>
===Introduction===
Adhesin Competence Regulator (<scene name='69/694230/Adcr_space_fill/1'>AdcR</scene>) is a transcriptional regulator that controls the activation of over seventy genes within the bacterium [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae''Streptococcus pneumoniae''] <ref name="Sanson">DOI:10.1093/nar/gku1304 </ref> and is a member of the multiple antibiotic resistance regulator (MarR) protein family <ref> PMID: 23428319</ref>. Members of the Mar R protein family conserve a number of features including a general triangular shape, a two fold pseudosymmetric homodimer, and a winged helix-turn-helix pattern [https://en.wikipedia.org/wiki/Helix-turn-helix (wHTH)] which can be seen in Figure 1. AdcR exhibits these conserved features as well, while also exhibiting its own distinct features.

[[Image:MarR_protein_family_slide.png|500px|left|thumb|'''Figure 1'''. Proteins MarR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3bpx (3BPX)], HucR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2FBK (2FBK)], TcaR [http://www.rcsb.org/pdb/explore/explore.do?structureId=3KP5 (3KP5)], and OhrR [http://www.rcsb.org/pdb/explore/explore.do?structureId=2pfb (2PFB)] are pictured above with conserved features of the MarR protein family highlighted]]
In contrast with other members of the MarR family, AdcR is metal dependent. Zinc plays a vital role in organism homeostasis, acting as a [https://en.wikipedia.org/wiki/Cofactor_(biochemistry) co-factor] and a regulator of enzymatic activity. However zinc can lead to cell toxicity and deficiency of other vital metals that are also necessary for protein function <ref> DOI: 10.1021/cr900077w</ref>. Binding of Zinc allows AdcR to bind DNA and activate the transcription of high-affinity Zinc specific uptake transporters. The importance of AdcR in ''Streptococcus pneumoniae'' can be understood provided its ability to regulate zinc transfer proteins within the bacteria.

==='''Structural Overview'''===
One of the two functional domains of AdcR is the <scene name='69/694230/Dimerization_domain/3'> dimerization domain</scene>. This domain connects and stabilizes the two pseudosymmetric protomers and is composed of the <scene name='69/694230/Alpha_1/1'>α1 helix</scene>, the <scene name='69/694230/Alpha_6/1'>α6 helix</scene> . and the C-terminus of the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> . This domain is connected to the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain] by the long α5 helix. The DNA binding domain interacts with the major and minor grooves of DNA via the <scene name='69/694230/Whth_4/7'>winged helix-turn-helix (wHTH)</scene> motif. The binding of Zinc to the <scene name='69/694230/2_binding_sites/4'>Zinc binding pocket</scene> induces a conformational change that allows for a <scene name='69/694230/Hydrogen_bonding_1/4'>hydrogen bond network</scene> between 4 specific residues. This network connects multiple helices from the metal binding pockets and DNA binding domain, and is believed play a critical role in the allosteric activation of AdcR, allowing the protein to bind exposed bases along the major and minor grooves of the DNA ligand <ref name="guerra">PMID:22085181</ref>. Thus, the protein is able to perform its biological function by activating transcription after binding DNA.

== '''DNA Binding''' ==
=== Helix-Turn-Helix Motif ===
[[Image:Screen Shot 2017-04-18 at 11.56.32 PM.png|300 px|right|thumb|'''Figure 2'''. A generic protein representing the [https://images.google.com/imgres?imgurl=https%3A%2F%2Fclassconnection.s3.amazonaws.com%2F838%2Fflashcards%2F2220838%2Fjpg%2Fasdf-144940F88BA53A918F3.jpg&imgrefurl=https%3A%2F%2Fwww.studyblue.com%2Fnotes%2Fnote%2Fn%2Flecture-13%2Fdeck%2F10226974&docid=qBvv1vgKeLTGcM&tbnid=3nuaRjPWKUBfqM%3A&vet=1&w=741&h=756&hl=en&source=sh%2Fx%2Fim wHTH] motif binding the major and minor groove of DNA similar to AdcR.]]
The AdcR MarR transcriptional regulator's structure resembles that of other proteins in the MarR family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif (Figure 2) that assists in binding DNA <ref name="guerra" />. The <scene name='69/694230/Whth_4/7'>winged helix turn helix</scene> motif is made up of the α3 and α4 helices along with <scene name='69/694230/Anti-parallel_beta_sheet/2'>anti-parallel β sheets</scene> on each side. There is one wHTH motif per monomer. The recognition helix, or the α4 helix, binds the major groove of DNA through [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions] between exposed bases <ref name="guerra" />. The wings of the helix bind the minor groove of DNA while the other helices stabilize the DNA and Protein upon binding. The two anti parallel β sheets contain several <scene name='69/694230/Positive_residues_on_wing_3/4'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA. The charge map (Figure 3) highlights the dark blue tips of the wHTH motif consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. The residues are only shown on the random loop of one monomer because the random loop on the other protein monomer <scene name='69/694230/Uncrystallized_loop/1'>was not crystallized</scene>.
== '''Zn(II) Binding''' ==
Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/2_binding_sites/4'>two binding sites for zinc</scene> on each of its two protomers and can bind a total of four Zn(II) ions. The <scene name='69/694230/Alpha1-alpha2_loop/2'>α1-α2 loop</scene> combined with the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> and <scene name='69/694230/Alpha_2/1'>α2 helix</scene> make up the <scene name='69/694230/Two_binding_sites/2'>metal binding sites</scene>. Each protomer has one high affinity site (Binding site 1; KZn1 = 1012 M; pH 8) and one low affinity binding site (Binding Site 2; KZn2 = 107 M; pH 8) <ref name="Reyes">PMID:20804771</ref>. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/5'>hydrogen bonding</scene> of H108 and E41.
=== Binding Site 1 ===
<scene name='69/694230/Binding_site_1/5'>Binding site 1</scene> consists of a distorted tetrahedral geometry around Zn(II). The four amino acids involved in zinc binding are E24, H42, H108, and H112. Binding site 1 is the only binding site that plays a significant role in the protein's regulatory function. The ability of binding site 1 to coordinate to the Zn(II) ion is pH dependent. At pH 6 the binding affinity for the Zn(II) ion is 109 - 1010 M-1, but at pH 8 the binding affinity increases to 1012 M-1 <ref name="Reyes" />. This is due to the charges on the histidines of the binding site. At pH 6, the histidines are positively charged and are not able to interact with the positively charged Zn(II) ion. However, at pH 8 the histidines are neutrally charged and are able to coordinate with Zn(II), which increases the overall binding affinity. The AdcR MarR transcriptional regulator is able to bind Co(II) in binding site 1 in a way that induces similar conformational changes to Zn(II) binding. Co(II) coordination in binding site 1 is able to allosterically activate DNA binding similarly to Zn(II) binding <ref name="guerra" />.

=== Binding Site 2 ===
<scene name='69/694230/Binding_site_2/4'>Binding site 2</scene> consists of a highly distorted tetrahedral geometry around the zinc ion. There are three amino acids involved in the binding of the zinc ion (C30, E41, and E107) as well as a water molecule (shown as a red sphere). If Cys30 in binding site 2 is mutated to an alanine, it will have no effect on the ability of the protein to bind DNA <ref name="guerra" />. Therefore, binding site 2 has no significant role in the ability of AdcR to bind to DNA and AdcR is still able to function with no zinc bound present in binding site 2. In fact, the presence of binding site 2 may simply be due to an excess of zinc during the crystallization process.

=== Hydrogen Bond Network ===
[[Image:Charge_map.jpg |300 px|right|thumb|'''Figure 3'''. A charge map of AdcR shows the general triangular shape and the positively charged area on the tips of the wHTH motif]]
The binding of zinc metals creates a hydrogen bond network within the protein that connects the metal binding sites and the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain]. The <scene name='69/694230/Hydrogen_bonding_1/5'>hydrogen bond network</scene> (<scene name='69/694230/Hydrogen_bonding_2/5'>with measurements</scene>) is represented by each atom type in the 3D model. The hydrogen bond network is characteristic of the MarR family as a whole. More importantly, the hydrogen bonding network connects the metal binding pockets to the α4 helix also known as the recognition helix. <scene name='69/694230/Recognition_helix/3'>Several residues</scene> in the recognition helix recognize a sequence of DNA that is unknown at the moment; however, scientists are aware that the hydrogen bond network acts as an allosteric activator for the protein to bind DNA. The hydrogen bond network connects the α2 and α4 helix via hydrogen bonding between specific residues. After zinc is bound, a glutamate (E24) residue from a random coil accepts a hydrogen bond from the carboxamide end of an asparagine (N38) residue from the α2 helix. Then, a glutamine (Q40) residue from α2 helix accepts a hydrogen bond from a serine (S74) residue from the α4 helix <ref name="guerra" />. The binding of zinc allows for these conformational changes that induces the binding of DNA in order to activate genes.
[[Image:H Bonding of DNA.png|300 px|left|thumb|'''Figure 4'''. The Hydrogen Bonding Network is shown with dotted green lines approximately 2.8 angstroms between residues.]]

== '''Medical Relevancy''' ==
Streptococcus pneumoniae, the host to AdcR, is a significant pathogenic bacterium. Although asymptomatic in healthy individuals, S. pneumoniae can lead to Bronchitis, meningitis conjunctivitis, or brain abscesses in those with weaker immune systems. Host regulation of zinc is often used to combat pathogens such as S. pneumoniae <ref name="Sanson" />. A better understanding of AdcR, the regulator that controls the transcription of zinc specific uptake transporters, could help to illuminate better mechanism for combating not only S. pneumoniae, but other comparable bacteria.

</StructureSection>

== References ==
<references/>