7DO7

Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(NAD and L-rhamnose bound-form)

Summary for 7DO7

• Entry DOI: 10.2210/pdb7do7/pdb
• Descriptor: Short-chain dehydrogenase/reductase SDR, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, beta-L-rhamnopyranose, ... (4 entities in total)
• Functional Keywords: l-rhamnose metabolism, nadp-dependentdehydrogenase, sdr protein family, oxidoreductase
• Biological source: Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
• Total number of polymer chains: 2
• Total formula weight: 57424.73

Authors

Yoshiwara, K.,Watanabe, Y.,Watanabe, S. (deposition date: 2020-12-12, release date: 2021-02-03, Last modification date: 2024-03-27)

Primary citation

Yoshiwara, K.,Watanabe, S.,Watanabe, Y.
Crystal structure of l-rhamnose 1-dehydrogenase involved in the nonphosphorylative pathway of l-rhamnose metabolism in bacteria.
Febs Lett., 595:637-646, 2021

PubMed Abstract: Several microorganisms can utilize l-rhamnose as a carbon and energy source through the nonphosphorylative metabolic pathway, in which l-rhamnose 1-dehydrogenase (RhaDH) catalyzes the NAD(P) -dependent oxidization of l-rhamnose to l-rhamnono-1,4-lactone. We herein investigated the crystal structures of RhaDH from Azotobacter vinelandii in ligand-free, NAD -bound, NADP -bound, and l-rhamnose- and NAD -bound forms at 1.9, 2.1, 2.4, and 1.6 Å resolution, respectively. The significant interactions with the 2'-phosphate group of NADP , but not the 2'-hydroxyl group of NAD , were consistent with a preference for NADP over NAD . The C5-OH and C6-methyl groups of l-rhamnose were recognized by specific residues of RhaDH through hydrogen bonds and hydrophobic contact, respectively, which contribute to the different substrate specificities from other aldose 1-dehydrogenases in the short-chain dehydrogenase/reductase superfamily.

PubMed: 33482017
DOI: 10.1002/1873-3468.14046

Experimental method

X-RAY DIFFRACTION (1.57 Å)