5X20

The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate

Summary for 5X20

• Entry DOI: 10.2210/pdb5x20/pdb
• Related: 3WFI 3WFJ
• Descriptor: 2-dehydropantoate 2-reductase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 2-oxidanylidene-2-phenylazanyl-ethanoic acid, ... (6 entities in total)
• Functional Keywords: rossmann fold, dehydrogenase, nadh binding, oxidoreductase
• Biological source: Enterococcus faecium DO
• Total number of polymer chains: 6
• Total formula weight: 213764.58

Authors

Furukawa, N.,Miyanaga, A.,Nakajima, M.,Taguchi, H. (deposition date: 2017-01-29, release date: 2017-04-05, Last modification date: 2023-11-22)

Primary citation

Furukawa, N.,Miyanaga, A.,Nakajima, M.,Taguchi, H.
The ternary complex structure of d-mandelate dehydrogenase with NADH and anilino(oxo)acetate.
Biochem. Biophys. Res. Commun., 486:665-670, 2017

PubMed Abstract: Enterococcus faecium NAD-dependent d-mandelate dehydrogenase (d-ManDH) belongs to a ketopantoate reductase (KPR)-related d-2-hydroxyacid dehydrogenase family, and exhibits broad substrate specificity toward bulky hydrophobic 2-ketoacids, preferring C3-branched substrates. The ternary complex structure of d-ManDH with NADH and anilino(oxo)acetate (AOA) revealed that the substrate binding induces a shear motion of the N-terminal domain along the C-terminal domain, following the hinge motion induced by the NADH binding, and allows the bound NADH molecule to form favorable interactions with a 2-ketoacid substrate. d-ManDH possesses a sufficiently wide pocket that accommodates the C3 branched side chains of substrates like KPR, but unlike the pocket of KPR, the pocket of d-ManDH comprises an entirely hydrophobic surface and an expanded space, in which the AOA benzene is accommodated. The expanded space mostly comprises a mobile loop structure, which likely modulates the shape and size of the space depending on the substrate.

PubMed: 28327357
DOI: 10.1016/j.bbrc.2017.03.088

Experimental method

X-RAY DIFFRACTION (2.4 Å)