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| | <StructureSection load='4tkm' size='340' side='right'caption='[[4tkm]], [[Resolution|resolution]] 2.67Å' scene=''> | | <StructureSection load='4tkm' size='340' side='right'caption='[[4tkm]], [[Resolution|resolution]] 2.67Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4tkm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TKM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4tkm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TKM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.67Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4tkl|4tkl]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tkm OCA], [http://pdbe.org/4tkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tkm RCSB], [http://www.ebi.ac.uk/pdbsum/4tkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tkm ProSAT]</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=4tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tkm OCA], [https://pdbe.org/4tkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tkm RCSB], [https://www.ebi.ac.uk/pdbsum/4tkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tkm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A075B5H4_9SPHN A0A075B5H4_9SPHN] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sphingomonas sp. a1]] | + | [[Category: Sphingomonas sp. A1]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Kawai, S]] | + | [[Category: Kawai S]] |
| - | [[Category: Mikami, B]] | + | [[Category: Mikami B]] |
| - | [[Category: Murata, K]] | + | [[Category: Murata K]] |
| - | [[Category: Takase, R]] | + | [[Category: Takase R]] |
| - | [[Category: Alginate metabolism]]
| + | |
| - | [[Category: Alpha/beta/alpha]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann-fold]]
| + | |
| - | [[Category: Short-chain dehydrogenase/reductase]]
| + | |
| Structural highlights
Function
A0A075B5H4_9SPHN
Publication Abstract from PubMed
The alginate-assimilating bacterium, Sphingomonas sp. strain A1, degrades the polysaccharides to monosaccharides through four alginate lyase reactions. The resultant monosaccharide, which is nonenzymatically converted to 4-deoxy-l-erythro-5-hexoseulose uronate (DEH), is further metabolized to 2-keto-3-deoxy-d-gluconate by NADPH-dependent reductase A1-R in the short-chain dehydrogenase/reductase (SDR) family. A1-R-deficient cells produced another DEH reductase, designated A1-R', with a preference for NADH. Here, we show the identification of a novel NADH-dependent DEH reductase A1-R' in strain A1, structural determination of A1-R' by x-ray crystallography, and structure-based conversion of a coenzyme requirement in SDR enzymes, A1-R and A1-R'. A1-R' was purified from strain A1 cells and enzymatically characterized. Except for the coenzyme requirement, there was no significant difference in enzyme characteristics between A1-R and A1-R'. Crystal structures of A1-R' and A1-R'.NAD(+) complex were determined at 1.8 and 2.7 A resolutions, respectively. Because of a 64% sequence identity, overall structures of A1-R' and A1-R were similar, although a difference in the coenzyme-binding site (particularly the nucleoside ribose 2' region) was observed. Distinct from A1-R, A1-R' included a negatively charged, shallower binding site. These differences were caused by amino acid residues on the two loops around the site. The A1-R' mutant with the two A1-R-typed loops maintained potent enzyme activity with specificity for NADPH rather than NADH, demonstrating that the two loops determine the coenzyme requirement, and loop exchange is a promising method for conversion of coenzyme requirement in the SDR family.
Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism.,Takase R, Mikami B, Kawai S, Murata K, Hashimoto W J Biol Chem. 2014 Nov 28;289(48):33198-214. doi: 10.1074/jbc.M114.585661. Epub, 2014 Oct 6. PMID:25288804[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Takase R, Mikami B, Kawai S, Murata K, Hashimoto W. Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism. J Biol Chem. 2014 Nov 28;289(48):33198-214. doi: 10.1074/jbc.M114.585661. Epub, 2014 Oct 6. PMID:25288804 doi:http://dx.doi.org/10.1074/jbc.M114.585661
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