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| | ==Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)== | | ==Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)== |
| - | <StructureSection load='2dgk' size='340' side='right' caption='[[2dgk]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='2dgk' size='340' side='right'caption='[[2dgk]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dgk]] is a 6 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=2DGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DGK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dgk]] is a 6 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=2DGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DGK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pmm|1pmm]], [[1pmo|1pmo]], [[2dgl|2dgl]], [[2dgm|2dgm]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gadB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2dgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dgk OCA], [https://pdbe.org/2dgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dgk RCSB], [https://www.ebi.ac.uk/pdbsum/2dgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dgk ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dgk OCA], [http://pdbe.org/2dgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dgk RCSB], [http://www.ebi.ac.uk/pdbsum/2dgk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dgk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DCEB_ECOLI DCEB_ECOLI] |
| | == 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: Capitani, G]] | + | [[Category: Capitani G]] |
| - | [[Category: Gruetter, M G]] | + | [[Category: Gruetter MG]] |
| - | [[Category: Gut, H]] | + | [[Category: Gut H]] |
| - | [[Category: Autoinhibition]]
| + | |
| - | [[Category: Gadb]]
| + | |
| - | [[Category: Gadbd1-14]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Substituted aldamine]]
| + | |
| Structural highlights
Function
DCEB_ECOLI
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
Escherichia coli and other enterobacteria exploit the H+ -consuming reaction catalysed by glutamate decarboxylase to survive the stomach acidity before reaching the intestine. Here we show that chloride, extremely abundant in gastric secretions, is an allosteric activator producing a 10-fold increase in the decarboxylase activity at pH 5.6. Cooperativity and sensitivity to chloride were lost when the N-terminal 14 residues, involved in the formation of two triple-helix bundles, were deleted by mutagenesis. X-ray structures, obtained in the presence of the substrate analogue acetate, identified halide-binding sites at the base of each N-terminal helix, showed how halide binding is responsible for bundle stability and demonstrated that the interconversion between active and inactive forms of the enzyme is a stepwise process. We also discovered an entirely novel structure of the cofactor pyridoxal 5'-phosphate (aldamine) to be responsible for the reversibly inactivated enzyme. Our results link the entry of chloride ions, via the H+/Cl- exchange activities of ClC-ec1, to the trigger of the acid stress response in the cell when the intracellular proton concentration has not yet reached fatal values.
Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB.,Gut H, Pennacchietti E, John RA, Bossa F, Capitani G, De Biase D, Grutter MG EMBO J. 2006 Jun 7;25(11):2643-51. Epub 2006 May 4. PMID:16675957[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gut H, Pennacchietti E, John RA, Bossa F, Capitani G, De Biase D, Grutter MG. Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB. EMBO J. 2006 Jun 7;25(11):2643-51. Epub 2006 May 4. PMID:16675957
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