Analysis of the quaternary structure, substrate specificity, and catalytic mechanism of valine dehydrogenase

The solution of the three-dimensional structure of Bacillus sphaericus leucine dehydrogenase has enabled us to undertake a homology-based modeling exercise on the sequence differences between the families of leucine (LeuDH) and valine (ValDH) dehydrogenases. This analysis indicates that the secondary structure elements in the core of the two domains of a single subunit of these enzymes are conserved, as are residues directly implicated in the recognition of the nucleotide cofactor and in catalysis. Comparison of the sequences indicates that the residues in the pocket accommodating the side chain of the amino acid substrate are conserved between these two enzymes, suggesting that the small differences in specificity arise from minor changes in molecular structure, possibly associated with shifts of the main chain rather than mutation of residues in the pocket itself. While B. sphaericus LeuDH is an octamer, both Streptomyces cinnamonensis and Streptomyces coelicolor ValDHs are dimers. The differences in quaternary structure can be understood in terms of the deletion in the latter of a C-terminal loop, which forms important interactions around the four-fold axis in LeuDH.