9x6n: Difference between revisions
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New page: '''Unreleased structure''' The entry 9x6n is ON HOLD Authors: Yoshida, H., Yoshihara, A. Description: Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-al... |
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==Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose== | |||
<StructureSection load='9x6n' size='340' side='right'caption='[[9x6n]], [[Resolution|resolution]] 1.56Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9x6n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9X6N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9X6N FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.56Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PSJ:D-PSICOSE'>PSJ</scene>, <scene name='pdbligand=PSV:ALPHA-D-PSICOFURANOSE'>PSV</scene>, <scene name='pdbligand=WEB:(2~{S},3~{R},4~{R},5~{R})-2-(hydroxymethyl)oxane-2,3,4,5-tetrol'>WEB</scene></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=9x6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9x6n OCA], [https://pdbe.org/9x6n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9x6n RCSB], [https://www.ebi.ac.uk/pdbsum/9x6n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9x6n ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Recombinant NAD(+)-dependent ribitol dehydrogenase derived from Klebsiella oxytoca (KoRdh) exhibits activity toward both ribitol and allitol. KoRdh catalyzes the NAD(+)-dependent oxidation of allitol to d-allulose and the NADH-dependent reduction of d-allulose to allitol. Notably, the flexible loop of KoRdh undergoes conformational changes upon NAD(+) and substrate binding. To elucidate the flexible loop's role in substrate recognition, we determined the X-ray structures of KoRdh alone and in complexes with NAD(+), d-allulose, or d-allose. Although d-allose is an aldose and not a substrate of KoRdh, it binds to KoRdh in the pyranose form, revealing the location of the substrate-binding site. Based on these structures, we propose a substrate recognition mechanism for KoRdh. Impact statement This research reveals an insight into a substrate recognition mechanism in the flexible region of ribitol dehydrogenase. Because ribitol dehydrogenase is a member of the short-chain reductases/oxidases (SDR) family, the current study will provide further insight into related enzymes that harbor the flexible region. | |||
Crystal structures of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD(+), d-allose, or d-allulose reveal insight into substrate recognition.,Yoshida H, Matsumoto M, Yamamoto N, Yoshihara A, Izumori K, Kamitori S FEBS Lett. 2026 Apr 21. doi: 10.1002/1873-3468.70345. PMID:42015598<ref>PMID:42015598</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 9x6n" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Klebsiella oxytoca]] | |||
[[Category: Large Structures]] | |||
[[Category: Yoshida H]] | |||
[[Category: Yoshihara A]] | |||
Latest revision as of 08:31, 29 April 2026
Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose
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