1bgv
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1bgv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BGV FirstGlance]. <br> | <table><tr><td colspan='2'>[[1bgv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BGV FirstGlance]. <br> | ||
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene></td></tr> |
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bgv OCA], [https://pdbe.org/1bgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bgv RCSB], [https://www.ebi.ac.uk/pdbsum/1bgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bgv ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bgv OCA], [https://pdbe.org/1bgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bgv RCSB], [https://www.ebi.ac.uk/pdbsum/1bgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bgv ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DHE2_CLOSY DHE2_CLOSY] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bgv ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bgv ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | We have solved the structure of the binary complex of the glutamate dehydrogenase from Clostridium symbiosum with glutamate to 1.9 A resolution. In this complex, the glutamate side-chain lies in a pocket on the enzyme surface and a key determinant of the enzymic specificity is an interaction of the substrate gamma-carboxyl group with the amino group of Lys89. In the apo-enzyme, Lys113 from the catalytic domain forms an important hydrogen bond to Asn373, in the NAD(+)-binding domain. On glutamate binding, the side-chain of this lysine undergoes a significant movement in order to optimize its hydrogen bonding to the alpha-carboxyl group of the substrate. Despite this shift, the interaction between Lys113 and Asn373 is maintained by a large-scale conformational change that closes the cleft between the two domains. Modelling studies indicate that in this "closed" conformation the C-4 of the nicotinamide ring and the alpha-carbon atom of the amino acid substrate are poised for efficient hydride transfer. Examination of the structure has led to a proposal for the catalytic activity of the enzyme, which involves Asp165 as a general base, and an enzyme-bound water molecule, hydrogen-bonded to an uncharged lysine residue, Lys125, as an attacking nucleophile in the reaction. | ||
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| - | Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.,Stillman TJ, Baker PJ, Britton KL, Rice DW J Mol Biol. 1993 Dec 20;234(4):1131-9. PMID:8263917<ref>PMID:8263917</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1bgv" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Glutamate dehydrogenase|Glutamate dehydrogenase]] | *[[Glutamate dehydrogenase|Glutamate dehydrogenase]] | ||
*[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]] | *[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Clostridium symbiosum]] | ||
| - | [[Category: Glutamate dehydrogenase]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Baker | + | [[Category: Baker PJ]] |
| - | [[Category: Britton | + | [[Category: Britton KL]] |
| - | [[Category: Rice | + | [[Category: Rice DW]] |
| - | [[Category: Stillman | + | [[Category: Stillman TJ]] |
| - | + | ||
Current revision
GLUTAMATE DEHYDROGENASE
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