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| | ==Crystal Structure of A12K/D35S mutant myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NADP== | | ==Crystal Structure of A12K/D35S mutant myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NADP== |
| - | <StructureSection load='4l8v' size='340' side='right' caption='[[4l8v]], [[Resolution|resolution]] 2.09Å' scene=''> | + | <StructureSection load='4l8v' size='340' side='right'caption='[[4l8v]], [[Resolution|resolution]] 2.09Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4l8v]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L8V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4l8v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L8V 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=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 2.09Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4l9r|4l9r]], [[3mz0|3mz0]], [[3nt2|3nt2]], [[3nt4|3nt4]], [[3nt5|3nt5]], [[3nto|3nto]], [[3ntq|3ntq]]</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=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU39700, E83G, idh, iolG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4l8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8v OCA], [https://pdbe.org/4l8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l8v RCSB], [https://www.ebi.ac.uk/pdbsum/4l8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8v 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=4l8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l8v OCA], [http://pdbe.org/4l8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l8v RCSB], [http://www.ebi.ac.uk/pdbsum/4l8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l8v 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> |
| | <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: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Inositol 2-dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bertwistle, D]] | + | [[Category: Bertwistle D]] |
| - | [[Category: Palmer, D R.J]] | + | [[Category: Palmer DRJ]] |
| - | [[Category: Sanders, D A.R]] | + | [[Category: Sanders DAR]] |
| - | [[Category: Binding site]]
| + | |
| - | [[Category: Catalysis]]
| + | |
| - | [[Category: Cofactor]]
| + | |
| - | [[Category: Hydrogen bonding]]
| + | |
| - | [[Category: Inositol]]
| + | |
| - | [[Category: Kinetic]]
| + | |
| - | [[Category: Nadp binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Sugar alcohol dehydrogenase]]
| + | |
| 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]
Publication Abstract from PubMed
myo-Inositol dehydrogenase (IDH, EC 1.1.1.18) from Bacillus subtilis converts myo-inositol to scyllo-inosose and is strictly dependent on NAD for activity. We sought to alter the coenzyme specificity to generate an NADP-dependent enzyme in order to enhance our understanding of coenzyme selectivity and to create an enzyme capable of recycling NADP in biocatalytic processes. Examination of available structural information related to the GFO/MocA/IDH family of dehydrogenases and precedents for altering coenzyme selectivity allowed us to select residues for substitution, and nine single, double, and triple mutants were constructed. Mutagenesis experiments with B. subtilis IDH proved extremely successful; the double mutant D35S/V36R preferred NADP to NAD by a factor of 5. This mutant is an excellent catalyst with a second-order rate constant with respect to NADP of 370 000 s(-1) M(-1), and the triple mutant A12K/D35S/V36R had a value of 570 000 s(-1) M(-1), higher than that of the wild-type IDH with NAD. The high-resolution X-ray crystal structure of the double mutant A12K/D35S was solved in complex with NADP. Surprisingly, the binding of the coenzyme is altered such that although the nicotinamide ring maintains the required position for catalysis, the coenzyme has twisted by nearly 90 degrees , so the adenine moiety no longer binds to a hydrophobic cleft in the Rossmann fold as in the wild-type enzyme. This change in binding conformation has not previously been observed in mutated dehydrogenases.
Converting NAD-Specific Inositol Dehydrogenase to an Efficient NADP-Selective Catalyst, with a Surprising Twist.,Zheng H, Bertwistle D, Sanders DA, Palmer DR Biochemistry. 2013 Aug 27;52(34):5876-83. doi: 10.1021/bi400821s. Epub 2013 Aug, 16. PMID:23952058[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
- ↑ Zheng H, Bertwistle D, Sanders DA, Palmer DR. Converting NAD-Specific Inositol Dehydrogenase to an Efficient NADP-Selective Catalyst, with a Surprising Twist. Biochemistry. 2013 Aug 27;52(34):5876-83. doi: 10.1021/bi400821s. Epub 2013 Aug, 16. PMID:23952058 doi:10.1021/bi400821s
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