3WFJ

The complex structure of D-mandelate dehydrogenase with NADH

Summary for 3WFJ

• Entry DOI: 10.2210/pdb3wfj/pdb
• Related: 3WFI
• Descriptor: 2-dehydropantoate 2-reductase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: rosmann fold, dehydrogenase, nadh binding, oxidoreductase
• Biological source: Enterococcus faecium
• Total number of polymer chains: 8
• Total formula weight: 280287.27

Authors

Miyanaga, A.,Fujisawa, S.,Furukawa, N.,Arai, K.,Nakajima, M.,Taguchi, H. (deposition date: 2013-07-19, release date: 2014-07-23, Last modification date: 2023-11-08)

Primary citation

Miyanaga, A.,Fujisawa, S.,Furukawa, N.,Arai, K.,Nakajima, M.,Taguchi, H.
The crystal structure of D-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase.
Biochem.Biophys.Res.Commun., 439:109-114, 2013

PubMed Abstract: D-Mandelate dehydrogenases (D-ManDHs), belonging to a new d-2-hydroxyacid dehydrogenase family, catalyze the conversion between benzoylformate and d-mandelate using NAD as a coenzyme. We determined the first D-ManDH structure, that of ManDH2 from Enterococcus faecalis IAM10071. The overall structure showed ManDH2 has a similar fold to 2-ketopantoate reductase (KPR), which catalyzes the conversion of 2-ketopantoate to d-pantoate using NADP as a coenzyme. They share conserved catalytic residues, indicating ManDH2 has the same reaction mechanism as KPR. However, ManDH2 exhibits significant structural variations in the coenzyme and substrate binding sites compared to KPR. These structural observations could explain their different coenzyme and substrate specificities.

PubMed: 23954635
DOI: 10.1016/j.bbrc.2013.08.019

Experimental method

X-RAY DIFFRACTION (2.8 Å)