Formate dehydrogenase active site

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... 

Scheme 6.1 Active sites of enzymes employing a double hydrogen-bonding motif for substrate coordination and activation in various biochemical transformations Haloalcohol dehalogenase (1), formate dehydrogenase (2), and serine protease (3).

Thus, an initial drop in ATP is followed by increases in Ca2+, which inhibits ATP synthase and increases ROS and reactive nitrogen species (RNS) formation via xanthine oxidase. These inhibit thiol-dependent Ca2+ transport. The reactive molecules can also inhibit the electron transport chain (by reacting with Fe at the active sites) and enzymes in glycolysis, notably glyceraldehyde 3-phosphate dehydrogenase, leading to further losses of ATP. The depleted ATP exacerbates the intracellular Ca2 increase as a result of reduced transport out and sequestration into the endoplasmic reticulum. 

Any discussion of the mechanism of xanthine oxidase should attempt to incorporate the special features of xanthine oxidase (and xanthine dehydrogenase and aldehyde oxidase) which are not present, for example, in sulfite oxidase. There are two such features at least (a) the involvement of two protons rather than the one found for sulfite oxidase, and (b) the presence of the cyanolyzable sulfur atom. The mechanistic features discussed so far involve the abstraction of two electrons and a proton. This means that a carbonium ion is generated, which could undergo attack by a nucleophile. Thus, the presence of a nucleophile at the active site could lead to the formation of a covalent intermediate that will break down to give the products.1032 The nucleophile could either be the cyanolyzable sulfur atom or a group associated with the second proton. A possible scheme is shown in Figure 41. 

Redox potentials of the molybdenum centers in several of the enzymes have been obtained by potentiometric titration (Table 3a). Although the substrate reaction chemistry requires the metal center to participate in net two-electron redox reactions, the simple electron-transfer reactions of the active sites occur in one-electron steps involving the MoVI/Mov and Mov/MoIV couples. Several of the molybdenum enzymes studied have MoVI/Mov and Mov/MoIV couples that differ by less than 40 mV. However, in sulfite oxidase the Movl/Mov (38 mV) and Mov/Molv (-239 mV) couples are separated by roughly 275 mV [88], In formate dehydrogenase (D. desulfuricans) the MoVI/Mov (-160 mV) and Mov/MoIV (-330 mV) couples are separated by 170 mV [89], Both the MoVI/Mov 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 [2Fe 2S], [3Fe S], and [4Fe S] clusters that are found in simple Fe S proteins are also constituents of respiratory and photosynthetic electron transport chains. Multicluster Fe S enzymes such as hydrogenase, formate dehydrogenase, NADH dehydrogenase, and succinate dehydrogenase feed electrons into respiratory chains, while others such as nitrate reductase, fhmarate reductase, DMSO reductase, and HDR catalyze the terminal step in anaerobic electron transport chains that utihze nitrate, fumarate, DMSO, and the CoB S S CoM heterodisulfide as the respiratory oxidant. All comprise membrane anchor polypeptide(s) and soluble subunits on the membrane surface that mediate electron transfer to or from Mo cofactor (Moco), NiFe, Fe-S cluster or flavin active sites. Multiple Fe-S clusters define electron transport pathways between the active site and the electron donor or... 

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. ... 

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