The Simple and Unique Allosteric Machinery of Thermus caldophilus Lactate Dehydrogenase

Abstract

Many bacterial L-lactate dehydrogenases (LDH) are allosteric enzymes, and usually activated by fructose 1,6-bisphosphate (FBP) and often also by substrate pyruvate. The active and inactive state structures demonstrate that Thermus caldophilus, Lactobacillus casei, and Bifidobacterium longum LDHs consistently undergo allosteric transition according to Monod-Wyman-Changeux model, where the active (R) and inactive (T) states of the enzymes coexist in an allosteric equilibrium (pre-existing equilibrium) independently of allosteric effectors. The three enzymes consistently take on open and closed conformations of the homotetramers for the T and R states, coupling the quaternary structural changes with the structural changes in binding sites for substrate and FBP though tertiary structural changes. Nevertheless, the three enzymes undergo markedly different structural changes from one another, indicating that there is a high variety in the allosteric machineries of bacterial LDHs. L. casei LDH undergoes the largest quaternary structural change in the three enzymes, and regulates its catalytic activity though a large linkage frame for allosteric motion. In contrast, T. caldophilus LDH exhibits the simplest allosteric motion in the three enzymes, involving a simple mobile structural core for the allosteric motion. TcLDH likely mediates its allosteric equilibrium mostly through electrostatic repulsion within the protein molecule, providing an insight for regulation machineries in bacterial allosteric LDHs.

The Conformational Plasticity Vista of PDZ Domains

“…These results show a direct correlation between the formation of the nuclei that leads to the native structure and ligand binding [10]. Numerous other examples have directly linked conformational states and binding [74][75][76][77]. Nevertheless, the PTP-BL PDZ2 analysis relates nonstable conformations (in the classical manner of open/close) but the folding process itself and binding.…”

Thermal activation of ‘allosteric-like’ large-scale motions in a eukaryotic Lactate Dehydrogenase

“…Because of their dynamical properties and allosteric behaviour, Lactate Dehydrogenase (EC 1.1.1.27) (LDH) is an appropriate enzyme model to decipher the motions involved in the conformational changes that regulate enzyme catalytic activity2829. Recent studies have also shown that targeting eukaryotic LDHs with inhibitors, is an efficient way to treat epilepsy and cancers3031.…”

Remote oxidative modifications induced by oxygen free radicals modify T/R allosteric equilibrium of a hyperthermophilic lactate dehydrogenase

“…LDHs are active tetramers of identical 30-35 kDa subunits. Most of the bacterial enzymes are allosteric displaying homotropic activation by the pyruvate and heterotopic activation by fructose 1,6-bisphosphate (FBP) (Taguchi, 2017). In contrast, eukaryotic LDHs are considered as non-allosteric.…”

“…To shed light on this peculiar phenomenon, we continued our investigations on Tt LDH by considering its allosteric properties. Indeed, Tt LDH is considered as a good representative of allosteric LDHs (Colletier et al, 2012;Coquelle et al, 2007;Taguchi, 2017). The native tetrameric state has four catalytic sites and two FBP-binding sites.…”

“…The chemical reaction catalyzed by LDHs is well documented; it involves the direct transfer of a hydride ion from C4 of the reduced nicotinamide group of NADH to C2 of pyruvate accompanied by the protonation of pyruvate's keto oxygen, the proton being supplied by His195 (Iwata and Ohta, 1993;Coquelle et al, 2007;Taguchi, 2017). The crystal structures of bacterial LDHs corresponding to the active (R) state have been determined in the presence of the substrate analog oxamate (Iwata and Ohta, 1993;Coquelle et al, 2007;Taguchi, 2017). They revealed interactions between important residues in the catalytic site and the substrate (Fig.…”