9X6M

Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allose

Summary for 9X6M

• Entry DOI: 10.2210/pdb9x6m/pdb
• Related: 9X6L
• Descriptor: Ribitol 2-dehydrogenase, beta-D-allopyranose (3 entities in total)
• Functional Keywords: rossmann fold, dehydrogenase, oxidoreductase
• Biological source: Klebsiella oxytoca
• Total number of polymer chains: 4
• Total formula weight: 114671.46

Authors

Yoshida, H.,Yoshihara, A. (deposition date: 2025-10-15, release date: 2026-04-29)

Primary citation

Yoshida, H.,Matsumoto, M.,Yamamoto, N.,Yoshihara, A.,Izumori, K.,Kamitori, S.
Crystal structures of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD + , d-allose, or d-allulose reveal insight into substrate recognition.
Febs Lett., 2026

PubMed Abstract: 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.

PubMed: 42015598
DOI: 10.1002/1873-3468.70345

Experimental method

X-RAY DIFFRACTION (1.73 Å)