Studies on the active center of D- and L-lactate dehydrogenases using oxamate-diaminohexyl-Sepharose affinity chromatography

Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward d- and l-2-chloropropionate

Halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. Notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the d-specific dehalogenase from Rhizobium sp. RCI (DehD), which acts on d-2-chloropropionate but not on its l-enantiomer. The catalytic residues of this dehalogenase responsible for its affinity toward d-2-chloropropionate have not been experimentally determined, although its three-dimensional crystal structure has been solved. For this study, we performed in silico docking and molecular dynamic simulations of complexes formed by this dehalogenase and d- or l-2-chloropropionate. Arg134 of the enzyme plays the key role in the stereospecific binding and Arg16 is in a position that would allow it to activate a water molecule for hydrolytic attack on the d-2-chloropropionate chiral carbon for release of the halide ion to yield l-2-hydroxypropionate. We propose that within the DehD active site, the NH group of Arg134 can form a hydrogen bond with the carboxylate of d-2-chloropropionate with a strength of ∼4 kcal/mol that may act as an acid–base catalyst, whereas, when l-2-chloropropionate is present, this bond cannot be formed. The significance of the present work is vital for rational design of this dehalogenase in order to confirm the involvement of Arg16 and Arg134 residues implicated in hydrolysis and binding of d-2-chloropropionate in the active site of d-specific dehalogenase from Rhizobium sp. RC1.

Insights into substrate binding by D-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus D-lactate dehydrogenase

BACKGROUND

D-Lactate dehydrogenases (D-LDHs) and L-lactate dehydrogenases (L-LDHs) catalyze a reaction differing only in the chirality of the product. Both enzymes utilize the same kind of amino acid side chains in substrate binding and catalysis. Models based on D-LDH-related enzymes propose that these side chains assume identical roles in both enzymes with their active sites related by a simple geometrical relationship such as a mirror plane.

RESULTS

The crystal structure of the homodimeric D-LDH from Lactobacillus pentosus has been determined to 2.6 A resolution by multiple isomorphous replacement methods and the resulting molecular model refined to an R-factor of 19.1%. Topologically, the enzyme is closely related to other D-2-ketoacid dehydrogenase enzymes. Each subunit comprises two domains enclosing a deep cleft containing the active site. Substrate binding and domain closure have been modelled.

CONCLUSIONS

Comparison of the D-LDH structure with other members of the protein family and with the L-specific enzyme has confirmed that no overall structural relationship exists between the L-LDH and D-LDH enzymes - they belong to distinct protein classes. The small size of the ketoacid substrate and the very restricted number of functionally appropriate side chains will constrain the choice of amino acids and their placement in the active site. Our models imply that although the same kinds of amino acids are involved in substrate binding their exact chemical role might differ in the two dehydrogenases.

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

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.

Cloning and expression of the gene for hydroxypyruvate reductase (D-glycerate dehydrogenase from an obligate methylotroph Hyphomicrobium methylovorum GM2

The gene encoding hydroxypyruvate reductase, catalyzing the asymmetric reduction of hydroxypyruvate to D-glycerate, and its flanking regions were isolated from a methylotrophic bacterium, Hyphomicrobium methylovorum GM2. Nucleotide sequencing of the recombinant plasmids revealed that the hydroxypyruvate-reductase gene codes for the 322-amino-acid protein with calculated molecular mass 35,726 Da. The sequence was confirmed by sequencing the intact enzyme and peptides obtained by digestion of the enzyme with Achromobacter proteinase I. The amino acid sequence of the enzyme showed similarity to members of the D-isomer-specific 2-hydroxyacid dehydrogenase family. The recombinant plasmid, which was constructed by ligation of the cloned gene and an expression vector pKK223-3, was introduced into Escherichia coli HB101. The recombinant enzyme purified from the transformed E. coli cells was indistinguishable from the enzyme isolated from H. methylovorum GM2 by immunological and enzymological analyses.

D-lactate dehydrogenase. Substrate specificity and use as a catalyst in the synthesis of homochiral 2-hydroxy acids

This note compares the substrate specificity of D-lactate dehydrogenase (D-LDH, EC 1.1.1.28) to that of L-lactate dehydrogenase (L-LDH, EC 1.1.1.27), illustrates three procedures that use D-LDH in synthesis and two methods for recycling NADH, and provides experimental details illustrating the use of D-LDH in organic synthesis.

Intramolecular hydride transfer of a combined coenzyme-substrate analog by D- and L-lactate dehydrogenases

The synthesis of 3-[(3-carboxy-3-oxopropyl)aminocarbonyl]pyridine adenine dinucleotide, a new combined analog of NADH and pyruvate with pyruvate covalently attached to the amide nitrogen atom of the dihydronicotinamide ring via an additional methylene group, is described. In the presence of D-lactate dehydrogenase from Limulus polyphemus, from Lactobacillus leichmannii, and L-lactate dehydrogenase from pig skeletal muscle a redox reaction takes place between the pyruvate moiety and the dihydropyridine ring of the analog. This reaction is shown to be intramolecular by competition experiments with pyruvate. Degradation of the reaction products reveals that the carbon-2 atom of the formed lactate side chain exhibits D configuration in each of these cases studied.

Purification of the flavoproteins 6-hydroxy-D- and 6-hydroxy-L-nicotine oxidase using hydrophobic affinity chromatography

A systematic study of the homologous series of omega-aminoalkyl-agaroses revealed differences in the affinities of 6-hydroxy-D- and 6-hydroxy-L-nicotine oxidase. In contrast to supports with nonpolar alkyl chains, omega-aminoalkyl-agarose showed high affinity towards the L-specific enzyme, while the D-specific oxidase was bound most firmly by omega-aminododecyl-agarose. 6-Hydroxy-L-nicotine oxidase could be desorbed by 1.3M NaCl only in the presence of the substrate L-6-hydroxynicotine. Using the omega-aminoalkyl-agarose, a complete separation of the enantiozymes was accomplished and an efficient purification procedure for both oxidases established.