User:Adrian Aldrich/Prokaryotic Glutamine Synthetase Pfam Domains Outline

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(New page: Prokaryotic Glutamine Synthetase Tertiary Structure: PFam domains -(describe structure of protein leading in to a single chain) -each chain contains 2 domains, the Glutamine synthetase be...)
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Prokaryotic Glutamine Synthetase Tertiary Structure: PFam domains
Prokaryotic Glutamine Synthetase Tertiary Structure: PFam domains
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-(describe structure of protein leading in to a single chain)
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Prokaryotic Glutamine Synthetase is a dodecamer, comprised of 12 identical polypeptide chains, organized as a dimer of two disk like pentamers. Each protomer contains 2 Pfam domains, the Beta Grasp domain and the catalytic domain, preceded by meanders of a few resides in length which link the protomers together in the dodecamers core.
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-each chain contains 2 domains, the Glutamine synthetase beta grasp domain, and the glutamine synthetase catalytic domain.
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-the two domains are preceeded by a meander of 3-24 residues that link the chains in the proteins core.
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Beta Grasp domain
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'''Beta Grasp domain'''
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-comprised of residues 43-123(verification needed for using structure viewer)
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The beta grasp domain is the N-terminal domain, extending from residues 13-94. This domain is responsible for binding ATP, Glutamate, and Ammonia. ATP binds first, activating the site for binding glutamate. (need a more thorough description if possible.)
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-binds glutamate, ammonia, and ATP
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<show protein alignment image>
<show protein alignment image>
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<show structure of the domain in viewer>
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<show structures of the domain w and without ligands bound>
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Catalytic domain
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'''Catalytic domain'''
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-comprised of residues 129-382
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The catalytic domain is the C-terminal domain, extending from residues 101-382.
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-how it functions is not described, more research is necessary here
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(mechanism is not described, more research is necessary here)
<show alignment image>
<show alignment image>
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<show structure of the domain in viewer>
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<show structures of the domain with and without ligands in viewer>
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Active site
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'''Active site'''
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-there are 10 active sites in the decamer of the protein, each formed from the beta grasp domain of one chain and the catalytic domain of the neighboring chain.
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The dodecamer contains 12 active sites total, each formed from the Beta grasp domain of one protomer and the Catalytic domain of the neighboring protomer.
<show relation between chains, domains, and active sites with viewer>
<show relation between chains, domains, and active sites with viewer>
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-describe visually the important aspects of the active site
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-describe visually the important aspects of the active site, residues binding interactions etc..(havent generated the scenes yet)
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<show active site and ligands relationship, may need multiple scenes>
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<show active site and ligands relationship, will need multiple scenes>
Replace the PDB id after the STRUCTURE_ and after PDB= to load
Replace the PDB id after the STRUCTURE_ and after PDB= to load
and display another structure.
and display another structure.
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{{STRUCTURE_3cin | PDB=3cin | SCENE= }}
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{{STRUCTURE_1lgr | PDB=1lgr | SCENE= }}

Revision as of 01:14, 8 December 2008

Prokaryotic Glutamine Synthetase Tertiary Structure: PFam domains

Prokaryotic Glutamine Synthetase is a dodecamer, comprised of 12 identical polypeptide chains, organized as a dimer of two disk like pentamers. Each protomer contains 2 Pfam domains, the Beta Grasp domain and the catalytic domain, preceded by meanders of a few resides in length which link the protomers together in the dodecamers core.

Beta Grasp domain The beta grasp domain is the N-terminal domain, extending from residues 13-94. This domain is responsible for binding ATP, Glutamate, and Ammonia. ATP binds first, activating the site for binding glutamate. (need a more thorough description if possible.) <show protein alignment image> <show structures of the domain w and without ligands bound>

Catalytic domain The catalytic domain is the C-terminal domain, extending from residues 101-382. (mechanism is not described, more research is necessary here)

<show alignment image> <show structures of the domain with and without ligands in viewer>


Active site The dodecamer contains 12 active sites total, each formed from the Beta grasp domain of one protomer and the Catalytic domain of the neighboring protomer. <show relation between chains, domains, and active sites with viewer> -describe visually the important aspects of the active site, residues binding interactions etc..(havent generated the scenes yet) <show active site and ligands relationship, will need multiple scenes>

Replace the PDB id after the STRUCTURE_ and after PDB= to load and display another structure.


PDB ID 1lgr

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1lgr, resolution 2.79Å ()
Ligands: ,
Activity: Glutamate--ammonia ligase, with EC number 6.3.1.2
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml


Proteopedia Page Contributors and Editors (what is this?)

Adrian Aldrich

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