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| | ==Crystal structure of the ISC domain of VibB in complex with isochorismate== | | ==Crystal structure of the ISC domain of VibB in complex with isochorismate== |
| - | <StructureSection load='3tg2' size='340' side='right' caption='[[3tg2]], [[Resolution|resolution]] 1.10Å' scene=''> | + | <StructureSection load='3tg2' size='340' side='right'caption='[[3tg2]], [[Resolution|resolution]] 1.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3tg2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TG2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3tg2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TG2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ISC:(5S,6S)-5-[(1-CARBOXYETHENYL)OXY]-6-HYDROXYCYCLOHEXA-1,3-DIENE-1-CARBOXYLIC+ACID'>ISC</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.101Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3tb4|3tb4]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ISC:(5S,6S)-5-[(1-CARBOXYETHENYL)OXY]-6-HYDROXYCYCLOHEXA-1,3-DIENE-1-CARBOXYLIC+ACID'>ISC</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VC_0771, vibB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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=3tg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tg2 OCA], [https://pdbe.org/3tg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tg2 RCSB], [https://www.ebi.ac.uk/pdbsum/3tg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tg2 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/Isochorismatase Isochorismatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.1 3.3.2.1] </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=3tg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tg2 OCA], [http://pdbe.org/3tg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tg2 RCSB], [http://www.ebi.ac.uk/pdbsum/3tg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tg2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VIBB_VIBCH VIBB_VIBCH]] Involved in the biosynthesis of the catechol siderophore vibriobactin. Vibriobactin is a chelating compound involved in transporting iron from the bacterial environment into the cell cytoplasm. | + | [https://www.uniprot.org/uniprot/VIBB_VIBCH VIBB_VIBCH] Involved in the biosynthesis of the catechol siderophore vibriobactin. Vibriobactin is a chelating compound involved in transporting iron from the bacterial environment into the cell cytoplasm. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillo virgola del koch trevisan 1884]] | + | [[Category: Large Structures]] |
| - | [[Category: Isochorismatase]] | + | [[Category: Vibrio cholerae]] |
| - | [[Category: Gu, L]] | + | [[Category: Gu L]] |
| - | [[Category: Huang, Y]] | + | [[Category: Huang Y]] |
| - | [[Category: Li, N]] | + | [[Category: Li N]] |
| - | [[Category: Liu, M]] | + | [[Category: Liu M]] |
| - | [[Category: Liu, S]] | + | [[Category: Liu S]] |
| - | [[Category: Liu, X]] | + | [[Category: Liu X]] |
| - | [[Category: Niu, B]] | + | [[Category: Niu B]] |
| - | [[Category: Wei, T]] | + | [[Category: Wei T]] |
| - | [[Category: Xu, S]] | + | [[Category: Xu S]] |
| - | [[Category: Zhang, C]] | + | [[Category: Zhang C]] |
| - | [[Category: Zhu, D]] | + | [[Category: Zhu D]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
VIBB_VIBCH Involved in the biosynthesis of the catechol siderophore vibriobactin. Vibriobactin is a chelating compound involved in transporting iron from the bacterial environment into the cell cytoplasm.
Publication Abstract from PubMed
The N-terminal isochorismatase (ISC) domain of VibB (VibB-ISC) catalyzes the vinyl ether hydrolysis of isochorismate to 2,3-dihydro-2,3-dihydroxybenzoate and pyruvate. Structures of the ISC domain and its complex with isochorismate have been determined at 1.35 and 1.10 A resolution, respectively. Two catalytic waters which were absent from previously reported homologous structures were observed adjacent to isochorismate and the catalytic residues (Asp35 and Lys118) in the VibB-ISC complex. Molecular-dynamics (MD) simulations starting with the structure of the VibB-ISC complex suggest that the catalytic waters contribute to the hydrolysis of the vinyl ether by participating in two reactions. Firstly, they may function as a general acid to protonate the Asp35 carboxylate prior to isochorismate protonation; secondly, one of the catalytic waters may be activated by the ionizable side chain of Asp35 to perform a nucleophilic attack on the intermediate carbocation/oxocarbonium ion. The positions of the waters are both significantly affected by the mutation of Asp35 and Lys118. The structural, biochemical and MD results reveal the residues that are involved in substrate binding and provide clues towards defining a possible mechanism.
Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction.,Liu S, Zhang C, Li N, Niu B, Liu M, Liu X, Wei T, Zhu D, Huang Y, Xu S, Gu L Acta Crystallogr D Biol Crystallogr. 2012 Oct;68(Pt 10):1329-38. Epub 2012 Sep, 13. PMID:22993087[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Liu S, Zhang C, Li N, Niu B, Liu M, Liu X, Wei T, Zhu D, Huang Y, Xu S, Gu L. Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction. Acta Crystallogr D Biol Crystallogr. 2012 Oct;68(Pt 10):1329-38. Epub 2012 Sep, 13. PMID:22993087 doi:http://dx.doi.org/10.1107/S090744491202848X
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