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| - | ==Crystal strcuture of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH== | + | ==Crystal structure of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH== |
| - | <StructureSection load='5z6t' size='340' side='right' caption='[[5z6t]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='5z6t' size='340' side='right'caption='[[5z6t]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Picst Picst]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z6T FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5z6t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Scheffersomyces_stipitis_CBS_6054 Scheffersomyces stipitis CBS 6054]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z6T FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">XYL1, PICST_89614 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=322104 PICST])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-xylose_reductase D-xylose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.307 1.1.1.307] </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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [https://pdbe.org/5z6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [https://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t ProSAT]</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=5z6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z6t OCA], [http://pdbe.org/5z6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z6t RCSB], [http://www.ebi.ac.uk/pdbsum/5z6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z6t ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XYL1_PICST XYL1_PICST]] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.<ref>PMID:3921014</ref> | + | [https://www.uniprot.org/uniprot/XYL1_PICST XYL1_PICST] Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.<ref>PMID:3921014</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: D-xylose reductase]] | + | [[Category: Large Structures]] |
| - | [[Category: Picst]] | + | [[Category: Scheffersomyces stipitis CBS 6054]] |
| - | [[Category: Kim, K J]] | + | [[Category: Kim KJ]] |
| - | [[Category: Son, H F]] | + | [[Category: Son HF]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Pentose metabolism]]
| + | |
| - | [[Category: Scheffersomyces stipitis]]
| + | |
| - | [[Category: Xylose reductase]]
| + | |
| Structural highlights
Function
XYL1_PICST Reduces D-xylose into xylitol. Has a preference for NADPH, but can also utilize NADH as cosubstrate.[1]
Publication Abstract from PubMed
Lignocellulosic biomass, of which D-xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D-xylose utilization, we determined the crystal structure of D-xylose reductase from Schefferzomyces stipitis (SsXR) at a 1.95 A resolution. We also determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. Phylogenetic tree analysis showed that AKR enzymes annotated with bacterial/archaeal XRs belonged to uncharacterized AKR families and might have no XR function, and yeast/fungi derived enzymes, which belong to the same group with SsXR, can be candidates for XR to increase xylose consumption.
Structural insight into D-xylose utilization by xylose reductase from Scheffersomyces stipitis.,Son HF, Lee SM, Kim KJ Sci Rep. 2018 Nov 28;8(1):17442. doi: 10.1038/s41598-018-35703-x. PMID:30487522[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Verduyn C, Van Kleef R, Frank J, Schreuder H, Van Dijken JP, Scheffers WA. Properties of the NAD(P)H-dependent xylose reductase from the xylose-fermenting yeast Pichia stipitis. Biochem J. 1985 Mar 15;226(3):669-77. PMID:3921014
- ↑ Son HF, Lee SM, Kim KJ. Structural insight into D-xylose utilization by xylose reductase from Scheffersomyces stipitis. Sci Rep. 2018 Nov 28;8(1):17442. doi: 10.1038/s41598-018-35703-x. PMID:30487522 doi:http://dx.doi.org/10.1038/s41598-018-35703-x
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