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| | <StructureSection load='3afm' size='340' side='right'caption='[[3afm]], [[Resolution|resolution]] 1.65Å' scene=''> | | <StructureSection load='3afm' size='340' side='right'caption='[[3afm]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3afm]] 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=3AFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AFM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3afm]] 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=3AFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AFM FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3afn|3afn]]</div></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]] 1.65Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">a1-R ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90322 Sphingomonas sp. A1])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-dehydro-3-deoxy-D-gluconate_6-dehydrogenase 2-dehydro-3-deoxy-D-gluconate 6-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.126 1.1.1.126] </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=3afm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3afm OCA], [https://pdbe.org/3afm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3afm RCSB], [https://www.ebi.ac.uk/pdbsum/3afm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3afm 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=3afm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3afm OCA], [https://pdbe.org/3afm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3afm RCSB], [https://www.ebi.ac.uk/pdbsum/3afm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3afm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/D6RU56_9SPHN D6RU56_9SPHN] |
| | == 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: 2-dehydro-3-deoxy-D-gluconate 6-dehydrogenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sphingomonas sp. a1]] | + | [[Category: Sphingomonas sp. A1]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Mikami, B]] | + | [[Category: Mikami B]] |
| - | [[Category: Murata, K]] | + | [[Category: Murata K]] |
| - | [[Category: Ochiai, A]] | + | [[Category: Ochiai A]] |
| - | [[Category: Takase, R]] | + | [[Category: Takase R]] |
| - | [[Category: Alpha/beta/alpha]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann-fold]]
| + | |
| Structural highlights
Function
D6RU56_9SPHN
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
In Sphingomonas sp. A1, alginate is degraded by alginate lyases to its constituent monosaccharides, which are nonenzymatically converted to an alpha-keto acid, namely, 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH). The properties of the DEH-metabolizing enzyme and its gene in strain A1 were characterized. In the presence of alginate, strain A1 cells inducibly produced an NADPH-dependent DEH reductase (A1-R) in their cytoplasm. Molecular cloning of the enzyme gene indicated that A1-R belonged to the short-chain dehydrogenase/reductase superfamily and catalyzed the conversion of DEH to 2-keto-3-deoxy-d-gluconic acid most efficiently at around pH 7.0 and 50 masculineC. Crystal structures of A1-R and its complex with NADP were determined at around 1.6A resolution by X-ray crystallography. The enzyme consists of three layers (alpha/beta/alpha), with a coenzyme-binding Rossmann fold. NADP is surrounded by positively charged residues, and Gly-38 and Arg-39 are crucial for NADP binding. Site-directed mutagenesis studies suggest that Ser-150, Tyr-164, and Lys-168 located around the Rossmann fold constitute the catalytic triad. To our knowledge, this is the first report on molecular cloning and structure determination of a bacterial DEH reductase responsible for alginate metabolism.
Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1.,Takase R, Ochiai A, Mikami B, Hashimoto W, Murata K Biochim Biophys Acta. 2010 May 27. PMID:20685299[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Takase R, Ochiai A, Mikami B, Hashimoto W, Murata K. Molecular identification of unsaturated uronate reductase prerequisite for alginate metabolism in Sphingomonas sp. A1. Biochim Biophys Acta. 2010 May 27. PMID:20685299 doi:10.1016/j.bbapap.2010.05.010
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