Catalysis dehydrogenase

Schiff base fonnation, photochemistry, protein partitioning, catalysis by chymotrypsin, lipase, peroxidase, phosphatase, catalase and alcohol dehydrogenase. 

Figure 1.9 Examples of functionally important intrinsic metal atoms in proteins, (a) The di-iron center of the enzyme ribonucleotide reductase. Two iron atoms form a redox center that produces a free radical in a nearby tyrosine side chain. The iron atoms are bridged by a glutamic acid residue and a negatively charged oxygen atom called a p-oxo bridge. The coordination of the iron atoms is completed by histidine, aspartic acid, and glutamic acid side chains as well as water molecules, (b) The catalytically active zinc atom in the enzyme alcohol dehydrogenase. The zinc atom is coordinated to the protein by one histidine and two cysteine side chains. During catalysis zinc binds an alcohol molecule in a suitable position for hydride transfer to the coenzyme moiety, a nicotinamide, [(a) Adapted from P. Nordlund et al., Nature 345 593-598, 1990.)...

Based on the action of thiamine pyrophosphate in catalysis of the pyruvate dehydrogenase reaction, suggest a suitable chemical mechanism for the pyruvate decarboxylase reaction in yeast ... 

Catalysis by flavoenzymes has been reviewed and various analogues of FAD have been prepared e.g. P -adenosine-P -riboflavin triphosphate and flavin-nicotinamide dinucleotide ) which show little enzymic activity. The kinetic constants of the interaction between nicotinamide-4-methyl-5-acetylimidazole dinucleotide (39) and lactic dehydrogenase suggest the presence of an anionic group near the adenine residue at the coenzyme binding site of the enzyme. ... 

Leimkiihler S, AL Stockert, K Igarashi, T Nishino, R Hille (2004) The role of active site glutamate residues in catalysis of Rhodobacter capsulatus xanthine dehydrogenase. J Biol Chem 279 40437-40444. 

Boyington JC, VN Gladyshev, SV Khangulov, TC Stadtman, PD Sun (1997) Crystal structure of formate dehydrogenase H catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Science 275 1305-1308. 

Dobbek H, L Gremer, R Kiefersauer, R Huber, O Meyer (2002) Catalysis at a dinuclear [CuSMo(=0)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution. Proc Natl Acad Sci USA 99 15971-15976. 

So little is known about molybdenum enzymes other than milk xanthine oxidase that there is little to be said by way of general conclusions. In all cases where there is direct evidence (except possibly for xanthine dehydrogenase from Micrococcus lactilyticus) it seems that molybdenum in the enzymes does have a redox function in catalysis. For the xanthine oxidases and dehydrogenases and for aldehyde oxidase, the metal is concerned in interaction of the enzymes with reducing substrates. However, for nitrate reductase it is apparently in interaction with the oxidizing substrate that the metal is involved. In nitrogenase the role of molybdenum is still quite uncertain. 

Zn -containing alcohol dehydrogenase Linum usitatassimum HNL (L//HNL) has an ADP-binding /3a[3 domain and catalytic domain containing two Zn2+, which are not directly involved in catalysis [17]. 

Hummel, W., Abokitse, K., Drauz, K. et al. (2003) Towards a large-scale asymmetric reduction process with isolated enzymes Expression of an (5)-alcohol dehydrogenase in E. coli and studies on the synthetic potential of this biocatalyst. Advanced Synthesis and Catalysis, 345 (1 + 2), 153-159. 

Analyses of enzyme reaction rates continued to support the formulations of Henri and Michaelis-Menten and the idea of an enzyme-substrate complex, although the kinetics would still be consistent with adsorption catalysis. Direct evidence for the participation of the enzyme in the catalyzed reaction came from a number of approaches. From the 1930s analysis of the mode of inhibition of thiol enzymes—especially glyceraldehyde-phosphate dehydrogenase—by iodoacetate and heavy metals established that cysteinyl groups within the enzyme were essential for its catalytic function. The mechanism by which the SH group participated in the reaction was finally shown when sufficient quantities of purified G-3-PDH became available (Chapter 4). 

Kurz and Frieden in 1977 and 1980 determined -secondary kinetic isotope effects for the unusual desulfonation reaction shown in Table 1, both in free solution and with enzyme catalysis by glutamate dehydrogenase. The isotope effects (H/D) were in the range of 1.14-1.20. At the time, the correct equilibrium isotope effect had not been reported and their measurements yielded an erroneous value... 

Yeast alcohol dehydrogenase, catalysis of oxidation by NAD of benzyl alcohol equilibrium interconversion of benzyl alcohol and benzaldehyde... 

Yeast alcohol dehydrogenase (YADH), catalysis of reduction by NADH of acetone formate dehydrogenase (FDH), oxidation by NAD of formate horse-liver alcohol dehydrogenase (HLAD), catalysis of reduction by NADH of cyclohexanone With label in NADH, the secondary KIE is 1.38 for reduction of acetone (YADH) with label in NAD, the secondary KIE is 1.22 for oxidation of formate (FDH) with label in NADH, the secondary KIE is 1.50 for reduction of cyclohexanone (HLAD). The exalted secondary isotope effects were suggested to originate in reaction-coordinate motion of the secondary center. 

A few years later, Cha, Murray and Klinman published a report on isotope effects in the redox interconversion of benzyl alcohol-benzaldehyde/NAD -NADH, with catalysis by yeast alcohol dehydrogenase. This article effected among biochemists... 

Fig. 6 Illustration from Chin and Klinman. Increased catalytic activity of horse-liver alcohol dehydrogenase in the oxidation of benzyl alcohol to benzaldehyde by NAD, measured by cat/ M (ordinate), correlates with the Swain-Schaad exponent for the -secondary isotope effect (abscissa), for which values above about four are indicators of tunneling. This is a direct test of the hypothesis that tunneling in the action of this enzyme contributes to catalysis. As the rate increases by over two orders of magnitude and then levels off, the anomalous Swain-Schaad exponents also increase and then level off. Reproduced from Ref. 28 with the permission of the American Chemical Society.

Moinuddin SGA, Youn B, Bedgar DL et al (2006) Secoisolariciresinol dehydrogenase mode of catalysis and stereospecificity of hydride transfer in Podophyllum peltatum. Org Biol Chem 4 808-816... 

Catalysis. Enzymes, with more than 2000 known representatives, are the largest group of proteins in terms of numbers (see p.88). The smallest enzymes have molecular masses of 10-15 kDa. Intermediatesized enzymes, such as alcohol dehydrogenase (top left) are around 100-200 kDa, and the largest-including glutamine synthetase with its 12 monomers (top right)—can reach more than 500 kDa. 

Proton transfers are particularly common. This acid-base catalysis by enzymes is much more effective than the exchange of protons between acids and bases in solution. In many cases, chemical groups are temporarily bound covalently to the amino acid residues of the enzyme or to coenzymes during the catalytic cycle. This effect is referred to as covalent catalysis (see the transaminases, for example p. 178). The principles of enzyme catalysis sketched out here are discussed in greater detail on p. 100 using the example of lactate dehydrogenase. 

The active center of an LDH subunit is shown schematically in Fig. 2. The peptide backbone is shown as a light blue tube. Also shown are the substrate lactate (red), the coenzyme NAD (yellow), and three amino acid side chains (Arg-109, Arg-171, and His-195 green), which are directly involved in the catalysis. A peptide loop (pink) formed by amino acid residues 98-111 is also shown. In the absence of substrate and coenzyme, this partial structure is open and allows access to the substrate binding site (not shown). In the enzyme lactate NAD"" complex shown, the peptide loop closes the active center. The catalytic cycle of lactate dehydrogenase is discussed on the next page. 

The principles of enzyme catalysis discussed on p. 90 can be illustrated using the reaction mechanism of lactate dehydrogenase (LDH) as an example. 

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