A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be
specific for the D-isomer of their substrate have been shown [1,2,3,4] to be
functionally and structurally related. These enzymes are listed below.
- D-lactate dehydrogenase (EC 1.1.1.28), a bacterial enzyme which catalyzes
the reduction of D-lactate to pyruvate.
- D-glycerate dehydrogenase (EC 1.1.1.29) (NADH-dependent hydroxypyruvate
reductase), a plant leaf peroxisomal enzyme that catalyzes the reduction of
hydroxypyruvate to glycerate. This reaction is part of the glycolate
pathway of photorespiration.
- D-glycerate dehydrogenase from the bacteria Hyphomicrobium methylovorum and
Methylobacterium extorquens.
- 3-phosphoglycerate dehydrogenase (EC 1.1.1.95), a bacterial enzyme that
catalyzes the oxidation of D-3-phosphoglycerate to 3-phosphohydroxypyruvate.
This reaction is the first committed step in the 'phosphorylated' pathway
of serine biosynthesis.
- Erythronate-4-phosphate dehydrogenase (EC 1.1.1.-) (gene pdxB), a bacterial
enzyme involved in the biosynthesis of pyridoxine (vitamin B6).
- D-2-hydroxyisocaproate dehydrogenase (EC 1.1.1.-) (D-hicDH), a bacterial
enzyme that catalyzes the reversible and stereospecific interconversion
between 2-ketocarboxylic acids and D-2-hydroxy-carboxylic acids.
- Formate dehydrogenase (EC 1.2.1.2) (FDH) from the bacteria Pseudomonas sp.
101 and various fungi [5].
- Vancomycin resistance protein vanH from Enterococcus faecium; this protein
is a D-specific α-keto acid dehydrogenase involved in the formation of
a peptidoglycan which does not terminate by D-alanine thus preventing
vancomycin binding.
- Escherichia coli hypothetical protein ycdW.
- Escherichia coli hypothetical protein yiaE.
- Haemophilus influenzae hypothetical protein HI1556.
- Yeast hypothetical protein YER081w.
- Yeast hypothetical protein YIL074w.
All these enzymes have similar enzymatic activities and are structurally
related. We have selected three of the most conserved regions of these
proteins to develop patterns. The first pattern is based on a glycine-rich
region located in the central section of these enzymes, this region probably
corresponds to the NAD-binding domain. The two other patterns contain a number
of conserved charged residues, some of which may play a role in the catalytic
mechanism.
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