Sandbox GGC5: Difference between revisions

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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.

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

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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.

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

[[Image: ~~Beta-~~lactam antibiotics ~~example 1~~.~~svg~~]]

Beta Lactam Ring present in Antibiotics

~~https://en.wikipedia.org/wiki/%CE%92-lactam_antibiotic#/media/File:Beta-lactam_antibiotics_example_1.svg~~

[[Image:Penicillin inhibition.svg]]

Penicillin inhibition

~~https://en.wikipedia.org/wiki/%CE%92-lactam_antibiotic#/media/File:Penicillin_inhibition.svg~~

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

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- 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>.

~~- 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>

-~~1,2 Ethanediol (EDO) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1~~ <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.

- 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>

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>

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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.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

== '''References''' ==

Sandbox GGC5: Difference between revisions

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@@ Line 2: / Line 2: @@
 <StructureSection load='3ZWF' size='340' side='right' caption='tRNAse Z Metallo-Beta Lactamase (homosapien)' scene=''>
 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.
 =='''Background Information'''==
@@ Line 9: / Line 8: @@
 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.
+[[Image:beta lactam ring in antibiotics.png]]
-[[Image: Beta-lactam antibiotics example 1.svg]]
 Beta Lactam Ring present in Antibiotics
-https://en.wikipedia.org/wiki/%CE%92-lactam_antibiotic#/media/File:Beta-lactam_antibiotics_example_1.svg
 [[Image:Penicillin inhibition.svg]]
 Penicillin inhibition
-https://en.wikipedia.org/wiki/%CE%92-lactam_antibiotic#/media/File:Penicillin_inhibition.svg
 =='''Mechanism of Antibiotic Beta Lactam Ring Resistance'''==
@@ Line 35: / Line 31: @@
 - 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>.
-- 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>
--1,2 Ethanediol (EDO) ligand on chains A and B of Zinc phosphodiesterase ELAC Protein 1 <ref>DOI 10.2210/pdb3ZWF/pdb</ref>.
+- 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>
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
 </StructureSection>
@@ Line 58: / Line 58: @@
 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.
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
 == '''References''' ==