Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure.

C Vinals; X De Bolle; E Depiereux; E Feytmans

doi:10.1002/prot.340210405

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Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure.

C Vinals·X De Bolle·E Depiereux·E Feytmans

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Abstract

A three-dimensional structure of the NAD-dependent D-lactate dehydrogenase of Lactobacillus bulgaricus is modeled using the structure of the formate dehydrogenase of Pseudomonas sp. as template. Both sequences share only 22% of identical residues. Regions for knowledge-based modeling are defined from the structurally conserved regions predicted by multiple alignment of a set of related protein sequences with low homology. The model of the D-LDH subunit shows, as for the formate dehydrogenase, an alpha/beta structure, with a catalytic domain and a coenzyme binding domain. It points out the catalytic histidine (His-296) and supports the hypothetical catalytic mechanism. It also suggests that the other residues involved in the active site are Arg-235, possibly involved in the binding of the carboxyl group of the pyruvate, and Phe-299, a candidate for stabilizing the methyl group of the substrate.

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Amino Acid Sequence Animals Binding Sites Dogfish L-Lactate Dehydrogenase Lactobacillus Models, Molecular Molecular Sequence Data Mutagenesis, Site-Directed NAD Protein Conformation Pyruvates Pyruvic Acid Comparative Study Journal Article

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C Vinals, X De Bolle, E Depiereux, E Feytmans. 1995. Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure.. https://doi.org/10.1002/prot.340210405

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