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| | ==Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor and product inosose== | | ==Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor and product inosose== |
| - | <StructureSection load='3nt5' size='340' side='right' caption='[[3nt5]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='3nt5' size='340' side='right'caption='[[3nt5]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nt5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NT5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NT5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nt5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NT5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NT5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ISE:(2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE'>ISE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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]] 2.9006Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mz0|3mz0]], [[3nt2|3nt2]], [[3nt4|3nt4]], [[3ntq|3ntq]], [[3ntr|3ntr]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ISE:(2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE'>ISE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU39700, E83G, idh, iolG, NP_391849.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3nt5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nt5 OCA], [https://pdbe.org/3nt5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nt5 RCSB], [https://www.ebi.ac.uk/pdbsum/3nt5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nt5 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/Inositol_2-dehydrogenase Inositol 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.18 1.1.1.18] </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=3nt5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nt5 OCA], [http://pdbe.org/3nt5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nt5 RCSB], [http://www.ebi.ac.uk/pdbsum/3nt5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nt5 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/IOLG_BACSU IOLG_BACSU]] Involved in the oxidation of myo-inositol (MI) and D-chiro-inositol (DCI) to 2-keto-myo-inositol (2KMI or 2-inosose) and 1-keto-D-chiro-inositol (1KDCI), respectively. Can also use D-glucose and D-xylose, and shows a trace of activity with D-ribose and D-fructose.<ref>PMID:112095</ref> <ref>PMID:16461681</ref> | + | [https://www.uniprot.org/uniprot/IOLG_BACSU IOLG_BACSU] Involved in the oxidation of myo-inositol (MI) and D-chiro-inositol (DCI) to 2-keto-myo-inositol (2KMI or 2-inosose) and 1-keto-D-chiro-inositol (1KDCI), respectively. Can also use D-glucose and D-xylose, and shows a trace of activity with D-ribose and D-fructose.<ref>PMID:112095</ref> <ref>PMID:16461681</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nt/3nt5_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nt/3nt5_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Inositol 2-dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Palmer, D R.J]] | + | [[Category: Palmer DRJ]] |
| - | [[Category: Sanders, D A.R]] | + | [[Category: Sanders DAR]] |
| - | [[Category: Straaten, K E.Van]] | + | [[Category: Van Straaten KE]] |
| - | [[Category: Bsidh]]
| + | |
| - | [[Category: Glyceraldehyde-3-phosphate like c-terminal domain]]
| + | |
| - | [[Category: Inositol]]
| + | |
| - | [[Category: Inosose]]
| + | |
| - | [[Category: N-terminal rossmann fold domain]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
IOLG_BACSU Involved in the oxidation of myo-inositol (MI) and D-chiro-inositol (DCI) to 2-keto-myo-inositol (2KMI or 2-inosose) and 1-keto-D-chiro-inositol (1KDCI), respectively. Can also use D-glucose and D-xylose, and shows a trace of activity with D-ribose and D-fructose.[1] [2]
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
Inositol dehydrogenase from Bacillus subtilis (BsIDH) is a NAD+-dependent enzyme that catalyses the oxidation of the axial hydroxyl group of myo-inositol to form scyllo-inosose. We have determined the crystal structures of wild type BsIDH and of the inactive K97V mutant in apo-, holo- and ternary complexes with inositol and inosose. BsIDH is a tetramer, with a novel arrangement consisting of 2 long continuous beta-sheets, formed from all 4 monomers, in which the central 2 strands are crossed over to form the core of the tetramer. Each subunit in the tetramer consists of two domains, an N-terminal Rossmann fold domain containing the cofactor-binding site, and a C-terminal domain containing the inositol-binding site. Structural analysis allowed us to determine residues important in cofactor and substrate binding. Lys97, Asp172, and His176 are the catalytic triad involved in the catalytic mechanism of BsIDH similar to what has been proposed for related enzymes and short chain dehydrogenases. Furthermore, a conformational change in the nicotinamide ring was observed in some ternary complexes, suggesting hydride transfer to the si-face of NAD+. Finally, comparison of the structure and sequence of BsIDH with other putative inositol dehydrogenases allowed us to differentiate these enzymes in four sub-families based on 6 consensus sequence motifs defining the cofactor- and substrate-binding sites.
Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification.,van Straaten KE, Zheng H, Palmer DR, Sanders DA Biochem J. 2010 Sep 1. PMID:20809899[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ramaley R, Fujita Y, Freese E. Purification and properties of Bacillus subtilis inositol dehydrogenase. J Biol Chem. 1979 Aug 25;254(16):7684-90. PMID:112095
- ↑ Yoshida K, Yamaguchi M, Morinaga T, Ikeuchi M, Kinehara M, Ashida H. Genetic modification of Bacillus subtilis for production of D-chiro-inositol, an investigational drug candidate for treatment of type 2 diabetes and polycystic ovary syndrome. Appl Environ Microbiol. 2006 Feb;72(2):1310-5. PMID:16461681 doi:http://dx.doi.org/72/2/1310
- ↑ van Straaten KE, Zheng H, Palmer DR, Sanders DA. Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification. Biochem J. 2010 Sep 1. PMID:20809899 doi:10.1042/BJ20101079
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