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1.1.1.345: D-2-hydroxyacid dehydrogenase (NAD+)

This is an abbreviated version!
For detailed information about D-2-hydroxyacid dehydrogenase (NAD+), go to the full flat file.

Word Map on EC 1.1.1.345

Reaction

an (R)-2-hydroxycarboxylate
+
NAD+
=
a 2-oxocarboxylate
 +
NADH
 +
H+

Synonyms

D-2-HADH, D-2-hydroxyacid dehydrogenase, D-2-hydroxyisocaproate dehydrogenase, D-HicDH, D-isomer specific 2-hydroxyacid dehydrogenase, D-isomer specific NAD+-dependent 2-hydroxyacid dehydrogenase, D-isomer-specific 2-hydroxyacid dehydrogenase, D-lactate dehydrogenase, D-lactate:NAD+ oxidoreductase, D-malate dehydrogenases, D-mandelate dehydrogenase, D-ManDH1, D-ManDH2, D-MDH, D2-HDH, HdhD, Ldb1010, ldh1837, LEUM_1837, ManDH2, NAD-dependent D-2-hydroxyacid dehydrogenase, PanE, R-HicDH

ECTree

     1 Oxidoreductases
         1.1 Acting on the CH-OH group of donors
             1.1.1 With NAD+ or NADP+ as acceptor
                1.1.1.345 D-2-hydroxyacid dehydrogenase (NAD+)

Crystallization

Crystallization on EC 1.1.1.345 - D-2-hydroxyacid dehydrogenase (NAD+)

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals are grown from a 1:1 mixture of a protein solution (10 mg/ml in 10 mM Tris–HCl (pH 7.5)) and a reservoir solution (0.085 M HEPES-Na (pH 7.5), 0.17 M ammonium acetate and 22.5% PEG8000) using the hanging-drop vapor diffusion method at 25°C. The overall structure shows that the enzyme has a similar fold to 2-ketopantoate reductase, which catalyzes the conversion of 2-ketopantoate to D-pantoate using NADP+ as a coenzyme. They share conserved catalytic residues, indicating that D-mandelate dehydrogenase ManDH2 has the same reaction mechanism as 2-ketopantoate reductase. However, D-mandelate dehydrogenase ManDH2 exhibits significant structural variations in the coenzyme and substrate binding sites compared to 2-ketopantoate reductase. These structural observations can explain their different coenzyme and substrate specificities
hanging drop vapor diffusion method, using 2.0-3.5 M ammonium sulfate or 14-26% PEG 3350 as precipitant
-
hexagonal crystals of recombinant D-HicDH in the presence of NAD+ and 2-oxoisocaproate (4-methyl-2-oxopentanoate) are grown with ammonium sulfate as precipitating agent. The structure of the crystals is solved by molecular replacement and refined to a final R-factor of 19.6% for all measured X-ray reflections in the resolution range 1.9 A resolution
vapor diffusion using ammonium sulfate as precipitant. The crystals belong to hexagonal space group type P6(3)22 with a = b = 134.1 A, c = 124.1 A and diffract X-rays to 3.0 A resolution. Packing considerations show that there are either one or two D-HicDH monomers in the asymmetric unit
purified enzyme in apoform and complexed with coenzyme NAD+, hanging drop vapor diffusion method, mixing of 400 nl of 10 mg/ml protein in 40 mM HEPES, pH 7.4, 300 mM NaCl, and 0.02% v/v monothioglycerol, with 400 nl reservoir solution containing 25% PEG 3350, 200 mM MgCl2, 100 mM HEPES, pH 7.5, and equilibration against 0.1 ml of reservoir solution at 19°C, crystals are supplemented with 10 mM NAD+ for the enzyme complex crystals, X-ray diffraction structure determination at 3.45 A and 2.75 A resolution, respectively, molecular replacement and modeling using the monomer structure of D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei, PDB ID 1DXY