Structural Insights into the Enzyme Mechanism of a New Family of D-2-Hydroxyacid Dehydrogenases, a Close Homolog of 2-Ketopantoate Reductase
Sukanta Mondal (suku@nibio.go.jp)
Kenji Mizuguchi (kenji@nibio.go.jp)
National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka 567-0085, Japan
Abstract
A newly identified family of NAD-dependent d-2-hydroxyacid
dehydrogenases (d-2-HydDHs) catalyzes the stereo-specific reduction of
branched-chain 2-keto acids with bulky hydrophobic side chains to
2-hydroxyacids. They are promising targets for industrial/practical
applications, particularly in the stereo-specific synthesis of
C3-branched d-hydroxyacids. Comparative modeling and docking studies
have been performed to build models of the enzyme-cofactor-substrate
complexes and identify key residues for cofactor and substrate
recognition. To explore large conformational transitions (domain
motions), a normal mode analysis was employed using a simple potential
and the protein models. Our analysis suggests that the new d-2-HydDH
family members possess the N-terminal NAD(H) binding Rossmann-fold
domain and the α-helical C-terminal substrate binding domain. A hinge bending motion between the N- and C-terminal domains was predicted, which would trigger the switch of the conserved essential Lys to form a key hydrogen bond with the C2 ketone of the 2-keto acid substrates. Our findings will be useful for site-directed mutagenesis studies and protein engineering.
Japanese Society for Bioinformatics