7WWX

Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehydrogenase (NAD bound form)

Summary for 7WWX

• Entry DOI: 10.2210/pdb7wwx/pdb
• Descriptor: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family), NICOTINAMIDE-ADENINE-DINUCLEOTIDE, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• Functional Keywords: l-arabinose metabolism, nad-dependent dehydrogenase, sdr protein family, oxidoreductase
• Biological source: Herbaspirillum huttiense subsp. putei IAM 15032
• Total number of polymer chains: 2
• Total formula weight: 60868.23

Authors

Matsubara, R.,Yoshiwara, K.,Watanabe, Y.,Watanabe, S. (deposition date: 2022-02-14, release date: 2022-03-30, Last modification date: 2023-11-29)

Primary citation

Watanabe, S.,Yoshiwara, K.,Matsubara, R.,Watanabe, Y.
Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein.
Biochem.Biophys.Res.Commun., 604:14-21, 2022

PubMed Abstract: l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P)-dependent oxidation of l-arabinose to L-arabinono-1,4-lactone in the non-phosphorylative l-arabinose pathway, and is classified into glucose-fructose oxidoreductase and short-chain dehydrogenase/reductase (SDR). We herein report the crystal structure of a SDR-type AraDH (from Herbaspirillum huttiense) for the first time. The interactions between Asp49 and the 2'- and 3'-hydroxyl groups of NAD were consistent with strict specificity for NAD. In a binding model for the substrate, Ser155 and Tyr168, highly conserved in the SDR superfamily, interacted with the C1 and/or C2 hydroxyl(s) of l-arabinose, whereas interactions between Asp107, Arg109, and Gln206 and the C2 and/or C3 hydroxyl(s) were unique to AraDH. Trp200 significantly contributed to the selectivities of the C4 hydroxyl and C6 methyl of substrates.

PubMed: 35279441
DOI: 10.1016/j.bbrc.2022.03.028

Experimental method

X-RAY DIFFRACTION (1.36 Å)