9x6o: Difference between revisions

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'''Unreleased structure'''


The entry 9x6o is ON HOLD
==Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD+==
<StructureSection load='9x6o' size='340' side='right'caption='[[9x6o]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9x6o]] 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=9X6O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9X6O 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]] 1.89&#8491;</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></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=9x6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9x6o OCA], [https://pdbe.org/9x6o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9x6o RCSB], [https://www.ebi.ac.uk/pdbsum/9x6o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9x6o 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.


Authors: Yoshida, H., Yoshihara, A.
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>


Description: Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Yoshihara, A]]
<div class="pdbe-citations 9x6o" style="background-color:#fffaf0;"></div>
[[Category: Yoshida, H]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Klebsiella oxytoca]]
[[Category: Large Structures]]
[[Category: Yoshida H]]
[[Category: Yoshihara A]]
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