Sandbox GGC5: Difference between revisions

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==~~Titin~~==

=='''Beta Lactamase'''==

~~This is a default text for your page '''Sandbox GGC5'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.~~

~~You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.~~

~~== Function ==~~

Beta Lactamase is a highly conserved enzyme in both prokaryotes and eukaryotes. In prokaryotes, it gives bacteria such as ''E.coli'' antibiotic resistance. In eukaryotes, it acts as exo and endonucleases to regulate transcription activity.

~~Titin~~ is a ~~key component~~ in ~~the assembly~~ and ~~function of vertebrate striated muscles~~. ~~Titin provides connections at the level of individual micro-filaments and contributes to the fine balance of forces between the two halves of the sarcomere~~. In ~~non-muscle cells~~, ~~titin plays a role in chromosome condensation~~ and ~~chromosome segregation during mitosis~~.

On the ~~cellular level~~, ~~titin~~ is ~~typically located within~~ the ~~nucleus of~~ the cell~~; however, it can also be located within the cytoplasm~~.

=='''Background Information'''==

~~== Disease ==~~

There are several classes of antibiotics, including cephalosporin and penicillin <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. Some common examples of specific drugs in these classes include cefazolin, cefadroxil, penicillin, ampicillin, and methicillin <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. These antibiotics function by preventing bacteria from forming their cell wall, regardless if the bacteria are gram positive or gram negative <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. These antibiotics all contain a beta-lactam ring <ref>https://doi.org/10.1021/cr030102i</ref>.

Inside of the gram positive or gram negative bacteria, there is a protein called the penicillin binding protein. The penicillin binding proteins (PBPs) are what help the peptidoglycan walls to form by linking NAG and NAM chains together. The beta-lactam ring fits particularly well into the PBP, which is how antibiotics like penicillin prevent bacteria from synthesizing its cell wall.

~~== Relevance ==~~

[[Image:beta lactam ring in antibiotics.png]]

Beta Lactam Ring present in Antibiotics

~~== Structural highlights ==~~

[[Image:Penicillin inhibition.svg]]

Penicillin inhibition

~~Secondary structure~~ <scene name='78/781193/~~Hydrophobic_structure_tc~~/1'>~~This is a secondary view~~ of the ~~titin structure~~.</scene>

=='''Mechanism of Antibiotic Beta Lactam Ring Resistance'''==

Bacteria such as ''E. coli'' make and excrete an enzyme called beta lactamase <ref>DOI: 10.1080/10409230701279118</ref>. Bacteria can become resistant to antibiotics that contain lactam rings when the B-lactamase enzyme attacks the beta lactam ring (classified as a hydrolase). Once the beta lactam ring is sliced open, it is no longer functional <ref> DOI 10.2210/pdb3ZWF/pdb </ref>.

=='''Beta Lactamase in Humans (PDB: 3ZWF)'''==

In order to make mature tRNAs, first they have to be processed <ref>https://doi.org/10.1101/575373</ref>. The enzyme that does tRNA processing is called TRNase Z. In humans, the form of beta lactamase formed uses a zinc-dependent mechanism, noted as metallo-beta lactamase <ref>DOI: 10.1080/10409230701279118</ref>. These enzymes in humans function to regulate nuclear activity, providing exo and endonuclease activity.

=='''Structural highlights'''==

Macromolecules:

Two chains (A,B) of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.

''Unique Ligands''

- Phosphate (PO4) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.

<scene name='78/781193/Po4/1'>PO4 Ligand</scene>

- Zinc (Zn) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.

<scene name='78/781193/2_zincs/1'>Zinc ions are adjacent to the phosphate to balance the charge</scene>

- 2007 hydrophobic amino acid residues <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.

<scene name='78/781193/Hydrophobic_amino_acids/1'>hydrophobic amino acid properties </scene>

- 1878 polar amino acid residues <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.

<scene name='78/781193/Polar_amino_acids/1'>polar amino acids</scene>

- Sodium (Na+) ion on chain B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.

<scene name='78/781193/Sodium_ion_enlarged/1'>Sodium Ion present</scene>

~~Secondary structure <scene name='78/781193/Complete_structure_tc/1'>This view of titin shows multiple structures contained in a titin band</scene>~~

</StructureSection>

== References ==

=='''Disease'''==

If there are mutations in the tRNase Z metallo-beta lactamases, these enzymes have been implicated in several diseases including prostate cancer <ref>DOI: 10.1080/10409230701279118</ref>. While there is still much to learn about how these lactamases work inter-connectedly with other enzymes, research suggests that metallo-beta lactamases function as cleavage and polyadenylation factors <ref>https://doi.org/10.1101/575373</ref>.

== '''Evolutionary Considerations''' ==

Beta Lactamase protein structure is highly conserved across both prokaryotes and eukaryotes <ref>doi: https://doi.org/10.1101/819797</ref>. Their presence indicates that these proteins are highly adaptable, with a wide range of substrates <ref>https://doi.org/10.1101/575373</ref>. The highly conserved nature of this structure suggests that the genetic material for beta lactamase is ancient in origin <ref>https://doi.org/10.1101/575373</ref>. They have found early beta lactamases in deep sea sediment, before the first antibiotic was ever encountered.

== '''References''' ==

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]

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@@ Line 1: / Line 1: @@
-==Titin==
+=='''Beta Lactamase'''==
-<StructureSection load='1TIT' size='340' side='right' caption='Caption for this structure' scene=''>
+<StructureSection load='3ZWF' size='340' side='right' caption='tRNAse Z Metallo-Beta Lactamase (homosapien)' scene=''>
-This is a default text for your page '''Sandbox GGC5'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
-== Function ==
+Beta Lactamase is a highly conserved enzyme in both prokaryotes and eukaryotes. In prokaryotes, it gives bacteria such as ''E.coli'' antibiotic resistance. In eukaryotes, it acts as exo and endonucleases to regulate transcription activity.
-Titin is a key component in the assembly and function of vertebrate striated muscles. Titin provides connections at the level of individual micro-filaments and contributes to the fine balance of forces between the two halves of the sarcomere. In non-muscle cells, titin plays a role in chromosome condensation and chromosome segregation during mitosis.
-On the cellular level, titin is typically located within the nucleus of the cell; however, it can also be located within the cytoplasm.
+=='''Background Information'''==
-== Disease ==
+There are several classes of antibiotics, including cephalosporin and penicillin <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. Some common examples of specific drugs in these classes include cefazolin, cefadroxil, penicillin, ampicillin, and methicillin <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. These antibiotics function by preventing bacteria from forming their cell wall, regardless if the bacteria are gram positive or gram negative <ref>doi: 10.1016/j.jmb.2019.04.002</ref>. These antibiotics all contain a beta-lactam ring <ref>https://doi.org/10.1021/cr030102i</ref>.
+Inside of the gram positive or gram negative bacteria, there is a protein called the penicillin binding protein. The penicillin binding proteins (PBPs) are what help the peptidoglycan walls to form by linking NAG and NAM chains together. The beta-lactam ring fits particularly well into the PBP, which is how antibiotics like penicillin prevent bacteria from synthesizing its cell wall.
-== Relevance ==
+[[Image:beta lactam ring in antibiotics.png]]
+Beta Lactam Ring present in Antibiotics
-== Structural highlights ==
+[[Image:Penicillin inhibition.svg]]
+Penicillin inhibition
-Secondary structure <scene name='78/781193/Hydrophobic_structure_tc/1'>This is a secondary view of the titin structure.</scene>
+=='''Mechanism of Antibiotic Beta Lactam Ring Resistance'''==
+Bacteria such as ''E. coli'' make and excrete an enzyme called beta lactamase <ref>DOI: 10.1080/10409230701279118</ref>. Bacteria can become resistant to antibiotics that contain lactam rings when the B-lactamase enzyme attacks the beta lactam ring (classified as a hydrolase). Once the beta lactam ring is sliced open, it is no longer functional <ref> DOI 10.2210/pdb3ZWF/pdb </ref>.
+=='''Beta Lactamase in Humans (PDB: 3ZWF)'''==
+In order to make mature tRNAs, first they have to be processed <ref>https://doi.org/10.1101/575373</ref>. The enzyme that does tRNA processing is called TRNase Z. In humans, the form of beta lactamase formed uses a zinc-dependent mechanism, noted as metallo-beta lactamase <ref>DOI: 10.1080/10409230701279118</ref>. These enzymes in humans function to regulate nuclear activity, providing exo and endonuclease activity.
+=='''Structural highlights'''==
+Macromolecules:
+Two chains (A,B) of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
+''Unique Ligands''
+- Phosphate (PO4) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
+<scene name='78/781193/Po4/1'>PO4 Ligand</scene>
+- Zinc (Zn) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
+<scene name='78/781193/2_zincs/1'>Zinc ions are adjacent to the phosphate to balance the charge</scene>
+- 2007 hydrophobic amino acid residues <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
+<scene name='78/781193/Hydrophobic_amino_acids/1'>hydrophobic amino acid properties </scene>
+- 1878 polar amino acid residues <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
+<scene name='78/781193/Polar_amino_acids/1'>polar amino acids</scene>
+- Sodium (Na+) ion on chain B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
+<scene name='78/781193/Sodium_ion_enlarged/1'>Sodium Ion present</scene>
-Secondary structure <scene name='78/781193/Complete_structure_tc/1'>This view of titin shows multiple structures contained in a titin band</scene>
 </StructureSection>
-== References ==
+=='''Disease'''==
+If there are mutations in the tRNase Z metallo-beta lactamases, these enzymes have been implicated in several diseases including prostate cancer <ref>DOI: 10.1080/10409230701279118</ref>. While there is still much to learn about how these lactamases work inter-connectedly with other enzymes, research suggests that metallo-beta lactamases function as cleavage and polyadenylation factors <ref>https://doi.org/10.1101/575373</ref>.
+== '''Evolutionary Considerations''' ==
+Beta Lactamase protein structure is highly conserved across both prokaryotes and eukaryotes <ref>doi: https://doi.org/10.1101/819797</ref>. Their presence indicates that these proteins are highly adaptable, with a wide range of substrates <ref>https://doi.org/10.1101/575373</ref>. The highly conserved nature of this structure suggests that the genetic material for beta lactamase is ancient in origin <ref>https://doi.org/10.1101/575373</ref>. They have found early beta lactamases in deep sea sediment, before the first antibiotic was ever encountered.
+== '''References''' ==
 <references/>
+[1]
+[2]
+[3]
+[4]
+[5]
+[6]
+[7]
+[8]