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| | <StructureSection load='1xey' size='340' side='right'caption='[[1xey]], [[Resolution|resolution]] 2.05Å' scene=''> | | <StructureSection load='1xey' size='340' side='right'caption='[[1xey]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1xey]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XEY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XEY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1xey]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XEY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GADA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GUA:GLUTARIC+ACID'>GUA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_decarboxylase Glutamate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.15 4.1.1.15] </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=1xey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xey OCA], [https://pdbe.org/1xey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xey RCSB], [https://www.ebi.ac.uk/pdbsum/1xey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xey ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xey OCA], [http://pdbe.org/1xey PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xey RCSB], [http://www.ebi.ac.uk/pdbsum/1xey PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xey ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DCEA_ECOLI DCEA_ECOLI]] Converts glutamate to gamma-aminobutyrate (GABA), consuming one intracellular proton in the reaction. The gad system helps to maintain a near-neutral intracellular pH when cells are exposed to extremely acidic conditions. The ability to survive transit through the acidic conditions of the stomach is essential for successful colonization of the mammalian host by commensal and pathogenic bacteria. | + | [https://www.uniprot.org/uniprot/DCEA_ECOLI DCEA_ECOLI] Converts glutamate to gamma-aminobutyrate (GABA), consuming one intracellular proton in the reaction. The gad system helps to maintain a near-neutral intracellular pH when cells are exposed to extremely acidic conditions. The ability to survive transit through the acidic conditions of the stomach is essential for successful colonization of the mammalian host by commensal and pathogenic bacteria. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Glutamate decarboxylase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Andreeva, N S]] | + | [[Category: Andreeva NS]] |
| - | [[Category: Darii, E L]] | + | [[Category: Darii EL]] |
| - | [[Category: Dutyshev, D I]] | + | [[Category: Dutyshev DI]] |
| - | [[Category: Fomenkova, N P]] | + | [[Category: Fomenkova NP]] |
| - | [[Category: Nikonov, S V]] | + | [[Category: Nikonov SV]] |
| - | [[Category: Pechik, I V]] | + | [[Category: Pechik IV]] |
| - | [[Category: Polyakov, K M]] | + | [[Category: Polyakov KM]] |
| - | [[Category: Sukhareva, B S]] | + | [[Category: Sukhareva BS]] |
| - | [[Category: Complex with glutarate]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
DCEA_ECOLI Converts glutamate to gamma-aminobutyrate (GABA), consuming one intracellular proton in the reaction. The gad system helps to maintain a near-neutral intracellular pH when cells are exposed to extremely acidic conditions. The ability to survive transit through the acidic conditions of the stomach is essential for successful colonization of the mammalian host by commensal and pathogenic bacteria.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Glutamate decarboxylase (GAD) is a pyridoxal enzyme that catalyzes the conversion of L-glutamate into gamma-aminobutyric acid and carbon dioxide. The Escherichia coli enzyme exists as two isozymes, referred to as GADalpha and GADbeta. Crystals of the complex of the recombinant isozyme GADalpha with glutarate as a substrate analogue were grown in space group R3, with unit-cell parameters a = b = 117.1, c = 196.4 angstroms. The structure of the enzyme was solved by the molecular-replacement method and refined at 2.05 angstroms resolution to an R factor of 15.1% (R(free) = 19.9%). The asymmetric unit contains a dimer consisting of two subunits of the enzyme related by a noncrystallographic twofold axis which is perpendicular to and intersects a crystallographic threefold axis. The dimers are related by a crystallographic threefold axis to form a hexamer. The active site of each subunit is formed by residues of the large domains of both subunits of the dimer. The coenzyme pyridoxal phosphate (PLP) forms an aldimine bond with Lys276. The glutarate molecule bound in the active site of the enzyme adopts two conformations with equal occupancies. One of the two carboxy groups of the glutarate occupies the same position in both conformations and forms hydrogen bonds with the N atom of the main chain of Phe63 and the side chain of Thr62 of one subunit and the side chains of Asp86 and Asn83 of the adjacent subunit of the dimer. Apparently, it is in this position that the distal carboxy group of the substrate would be bound by the enzyme, thus providing recognition of glutamic acid by the enzyme.
Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution.,Dutyshev DI, Darii EL, Fomenkova NP, Pechik IV, Polyakov KM, Nikonov SV, Andreeva NS, Sukhareva BS Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):230-5. Epub 2005, Feb 24. PMID:15735332[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dutyshev DI, Darii EL, Fomenkova NP, Pechik IV, Polyakov KM, Nikonov SV, Andreeva NS, Sukhareva BS. Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution. Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):230-5. Epub 2005, Feb 24. PMID:15735332 doi:10.1107/S0907444904032147
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