Formate dehydrogenase active site structure

Examination of the molecular dynamics (MD) simulation dehydrogenases with substrate and NAD(P)H at the active site shows that only one of the possible quasi-boat conformations exists (Bruice and Lightstone, 1998). The NAC structure in the lactate dehydrogenase active site is associated with the formation of the quasi-boat conformation. In this configuration the distance between the transferring hydride and pyruvate carbonyl is about 1 A shorter when the dihydropyridin ring is in the boat form than in the planar conformation. The closeness of the approach of the reactants in this pretransition state, and... 

Fig. 2.13 illustrates the electrostatic effects in transition state in enolase reaction (Larson et al., 1996). During this reaction a proton is removed by Lys-345 from C-2 of 2-phosphoglycerate to give an enolyzed, charged intermediate. This intermediate is stabilized by electrostatic interaction with five positive charges supplied by two Mg+2 ions and a protonated lysine. The 10-11 electrostatic interactions were found in the transition state of formate dehydrogenase and carbamoyl synthetase (Bruice and Benkovic, 2000) Another example of multifunctional interactions during enzymatic reactions in intermediate is the X-ray structure of tetrahedral intermediate in the chymotrypsin active site (Fig. 1.1). 

The structure of another member of this family, the selenocysteine-containing formate dehydrogenase H from E. coli, has also been determined it contains an [Mo 0(SeCys)(MGD)2] oxidized active site see Selenium Proteins Containing Selenocysteine). Formate dehydrogenases catalyze the interconversion of formate and carbon dioxide and play an important role in global fixation of carbon dioxide. ... 

Figure 7 Structure of the active site of iipoamide dehydrogenase from Pseudomonas putida. The key disulfide bond between Cys43 and Cys48 is shown in stick format, as is the fiavin cofactor and conserved amino acid Tyr181. The structure was prepared using the PyMOL Moiecuiar Graphics (http //www.pymoi.org).

The next step in coenzyme M formation is the dephosphorylation of phosphosulfolactate by a Mg(II)-dependent acid phosphatase, ComB. The third enzyme in the pathway, sulfolactate dehydrogenase (ComC), has also been structurally characterized with the bound reaction product NADH. ComC is present in solution as a dimer, and in the crystal the asymmetric unit contains a tetramer of tight dimers. The dimer is the enzymatically active unit and a portion of each monomer binds NADH at the active site. As a result of this interaction, ComC does not contain the classic Rossmann-Fold topology for NADH binding but instead defines a novel fold for NADH binding. 

The Zn ion, among the series of transition metals, is a cofactor which is not involved in redox reactions under physiological conditions. As a Lewis acid similar in strength to Mg , Zn participates in similar reactions. Hence, substituting the Zn ion for the Mg ion in some enzymes is possible without loss of enzyme activity. Both metal ions can function as stabilizers of enzyme conformation and their direct participation in catalysis is readily revealed in the case of alcohol dehydrogenase. This enzyme isolated from horse liver consists of two identical polypeptide chains, each with one active site. Two of the four Zn ions in the enzyme readily dissociate. Although this dissociation has no effect on the quaternary structure, the enzyme activity is lost. As described under section 2.3.1.1, both of these Zn ions are involved in the formation of the active site. In catalysis they polarize the substrate s C—O linkage and, thus, facilitate the transfer of hydride ions from or to the cosubstrate. Unlike the dissociable ions, removal of the two residual Zn ions is possible only under drastic conditions, namely disruption of the enzyme s quaternary structure which is maintained by these two ions. 

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