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
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{{STRUCTURE_1lgr | PDB=1lgr | SCENE= }}
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'''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 hexamers. Each protomer contains 2 Pfam domains, the Beta-grasp domain and the catalytic domain, preceded at the N terminus by short chains(3-13)of resides which link the all 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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-comprised of residues 43-123(verification needed for using structure viewer)
 
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-binds glutamate, ammonia, and ATP
 
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<show protein alignment image>
 
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<show structure of the domain in viewer>
 
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Catalytic domain
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'''Beta Grasp domain'''
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-comprised of residues 129-382
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-how it functions is not described, more research is necessary here
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<show alignment image>
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The <scene name='User:Adrian_Aldrich/Prokaryotic_Glutamine_Synthetase_Pfam_Domains_Outline/Betagrasp/1'>Beta-Grasp Domain</scene> is the N-terminal domain, extending from residues 13-94. This domain is responsible for binding ATP, Glutamate, and Ammonia. The domain folds into a bent beta-sheet flanked by two short alpha helices, forming a pocket for the ligands to bind. ATP binds first, activating the site for binding glutamate.
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<show structure of the domain in viewer>
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Active site
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'''Catalytic domain'''
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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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<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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<show active site and ligands relationship, may need multiple scenes>
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Replace the PDB id after the STRUCTURE_ and after PDB= to load
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The <scene name='User:Adrian_Aldrich/Prokaryotic_Glutamine_Synthetase_Pfam_Domains_Outline/Catalytic/1'>Catalytic Domain</scene> is the C-terminal domain, extending from residues 101-382, and forms a melon rind shaped thin beta sheet coated on one side by several alpha helices.
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and display another structure.
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{{STRUCTURE_3cin | PDB=3cin | SCENE= }}
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'''Active site'''
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The dodecamer contains 12 <scene name='User:Adrian_Aldrich/Prokaryotic_Glutamine_Synthetase_Pfam_Domains_Outline/Active_site/1'> Active sites</scene> in total, each formed from the Beta-grasp domain of one protomer and the Catalytic domain of the neighboring protomer. The concave beta sheet of the Catalytic domain( in green ) faces the pocket of the neighboring Beta-grasp domain( in red ), creating a funnel shaped hollow in which binding and catalysis is performed.

Current revision

PDB ID 1lgr

Drag the structure with the mouse to rotate
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


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 hexamers. Each protomer contains 2 Pfam domains, the Beta-grasp domain and the catalytic domain, preceded at the N terminus by short chains(3-13)of resides which link the all protomers together in the dodecamers core.


Beta Grasp domain

The is the N-terminal domain, extending from residues 13-94. This domain is responsible for binding ATP, Glutamate, and Ammonia. The domain folds into a bent beta-sheet flanked by two short alpha helices, forming a pocket for the ligands to bind. ATP binds first, activating the site for binding glutamate.


Catalytic domain

The is the C-terminal domain, extending from residues 101-382, and forms a melon rind shaped thin beta sheet coated on one side by several alpha helices.


Active site

The dodecamer contains 12 in total, each formed from the Beta-grasp domain of one protomer and the Catalytic domain of the neighboring protomer. The concave beta sheet of the Catalytic domain( in green ) faces the pocket of the neighboring Beta-grasp domain( in red ), creating a funnel shaped hollow in which binding and catalysis is performed.

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Adrian Aldrich

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