The oxaloacetate reductase activity of vertebrate lactate dehydrogenase

An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases

Malate and lactate dehydrogenases (MDH and LDH) are homologous, core metabolic enzymes that share a fold and catalytic mechanism yet possess strict specificity for their substrates. In the Apicomplexa, convergent evolution of an unusual LDH from MDH produced a difference in specificity exceeding 12 orders of magnitude. The mechanisms responsible for this extraordinary functional shift are currently unknown. Using ancestral protein resurrection, we find that specificity evolved in apicomplexan LDHs by classic neofunctionalization characterized by long-range epistasis, a promiscuous intermediate, and few gain-of-function mutations of large effect. In canonical MDHs and LDHs, a single residue in the active-site loop governs substrate specificity: Arg102 in MDHs and Gln102 in LDHs. During the evolution of the apicomplexan LDH, however, specificity switched via an insertion that shifted the position and identity of this 'specificity residue' to Trp107f. Residues far from the active site also determine specificity, as shown by the crystal structures of three ancestral proteins bracketing the key duplication event. This work provides an unprecedented atomic-resolution view of evolutionary trajectories creating a nascent enzymatic function.

Rational construction of a 2-hydroxyacid dehydrogenase with new substrate specificity

Using site-directed mutagenesis on the lactate dehydrogenase gene from Bacillus stearothermophilus, three amino acid substitutions have been made at sites in the enzyme which we suggest in part determine specificity toward different hydroxyacids (R-CHOH-COOH). To change the preferred substrates from the pyruvate/lactate pair (R = -CH3) to the oxaloacetate/malate pair (R = -CH2-COO-), the volume of the active site was increased (thr 246----gly), an acid was neutralized (asp-197----asn) and a base was introduced (gln-102 - greater than arg). The wild type enzyme has a catalytic specificity for pyruvate over oxaloacetate of 1000 whereas the triple mutant has a specificity for oxaloacetate over pyruvate of 500. Despite the severity and extent of these active site alterations, the malate dehydrogenase so produced retains a reasonably fast catalytic rate constant (20 s-1 for oxaloacetate reduction) and is still allosterically controlled by fructose-1,6-bisphosphate.

The use of site-directed mutagenesis and time-resolved fluorescence spectroscopy to assign the fluorescence contributions of individual tryptophan residues in Bacillus stearothermophilus lactate dehydrogenase

Site-directed mutagenesis has been used to generate two mutant Bacillus stearothermophilus lactate dehydrogenases: in one, Trp-150 has been replaced with a tyrosine residue and, in the other, both Trp-150 and -80 are replaced with tyrosines. Both enzymes are fully catalytically active and their affinities for substrates and coenzymes, and thermal stabilities are very similar to those of the native enzyme. Time-resolved fluorescence measurements using a synchrotron source have shown that all three tryptophans in the native enzyme fluoresce. By comparing the mutant and native enzymes it was possible, for the first time, to assign, unambiguously, lifetimes to the individual tryptophans: Trp-203 (7.4 ns), Trp-80 (2.35 ns) and Trp-150 (less than 0.3 ns). Trp-203 is responsible for 75-80% of the steady-state fluorescence emission, Trp-80 for 20%, and Trp-150 for less than 2%.

NAD-linked L(+)-lactate dehydrogenase from the strict aerobe alcaligenes eutrophus. 2. Kinetic properties and inhibition by oxaloacetate

The L(+)-lactate dehydrogenase (EC 1.1.1.27) of Alcaligenes eutrophus catalyzes the NADH-dependent reduction of pyruvate and a few other 2-oxoacids. The Km values for NADH, NAD, pyruvate and L(+)-lactate are 0.075 mM, 0.130 mM, 0.820 mM and 7.10 mM, respectively. The reaction follows a rapid equilibrium ordered bi-bi mechanism and involves the formation of a dead-end EBQ complex. The competitive inhibition of pyruvate reduction caused by NAD (with respect to NADH) is regarded to be of physiological importance. The enzyme is strongly inhibited by oxaloacetate, oxalate and to a less extent by oxamate. Oxaloacetate was found to be the most powerful inhibitor of the enzyme and exerts an almost complete inhibition of the reduction of pyruvate and some 2-oxoacids at concentrations of 1 microM and less. At 0.1 microM oxaloacetate the inhibition of pyruvate reduction is about 90%. The kinetics of pyruvate reduction in the presence of oxaloacetate is characterized by a burst phase followed by a decreased steady-state velocity. During the burst phase, which lasts from several seconds to some minutes, the enzyme undergoes transition to a less active enzyme form. The inhibition studies revealed the lactate dehydrogenase to be a hysteretic enzyme, due to its slow response to the ligand. The characteristics of the transient were examined. The inhibition of lactate dehydrogenase from A. eutrophus by oxaloacetate is considered to be of great physiological importance, allowing its function only at a low oxaloacetate concentration and consequently at high NADH/NAD ratios.

Slow structural changes shown by the 3-nitrotyrosine-237 residue in pig heart [Tyr(3NO2)237] lactate dehydrogenase

1. The pKa of the phenolic hydroxy group of the Tyr(3NO2)-237 residue in pig heart [Tyr(3NO2)237]lactate dehydrogenase is 7.2 in the apoenzyme, 7.4 in the enzyme-NADH complex and 7.8 in the enzyme-NADH-oxamate complex. The alkaline shift from apoenzyme to ternary complex is ascribed to the approach of the Glu-107 residue during the movement of the polypeptide loop residues 98-110. 2. The affinities of the nitrated enzyme for NADH and for oxamate (in the presence of NADH) are slightly less than those of the native enzyme. The turnover number for the nitrated enzyme in the pyruvate-to-lactate direction is about 0.75 of the value for the native enzyme. 3. Temperature-jump relaxation experiments of the enzyme saturated with NADH but fractionally saturated with oxamate are interpreted to show that the pKa of the nitrotyrosine residue responds to a protein rearrangement after oxamate binds to the binary enzyme-NADH complex. 4. Transient-kinetic experiments show the environment of the Tyr(3NO2)-237 residue in the enzyme-NADH-pyruvate complex of the steady state to be similar to that in the enzyme-NADH-oxamate inhibitor complex.