Coenzyme-substrate analogue

U. Grau, H. Kapmeyer, and W. E. Trommer (1978), Combined coenzyme-substrate analogues of various dehydrogenases. Synthesis of (3S)- and (3R)-5-(3-carboxy-3-hydroxypropyl) nicotinamide adenine dinucleotide and their interaction with (S)- and (R)-lactate-specific dehydrogenases. Biochemistry 17, 4621-4626. 

Several crystal structures of the enzyme in the presence of the coenzyme and substrate or substrate analogues have served as important indicators of the role of the coenzyme in the enzymic reaction. A crystal structure of the enzyme in the presence of NAD+ and p-bromobenzyl alcohol as substrate revealed that the oxygen of the alcohol is directly bound to the catalytic zinc, thus putting the carbon 1 of the alcohol 3.5 A from carbon 4 of the nicotinamide ring the substrate is thus positioned ideally for direct transfer of hydrogen. The position of the alcohol is close to where the water molecule is bound in the free enzyme, but it was not possible to establish whether this had been displaced on binding of the substrate.1364... 

Fig. 26. (A) Schematic diagram of one subunit of horse liver alcohol dehydrogenase. Znl is the active-site zinc. Designed by B. Furugren, from the work of Branden and colleagues [55], (B) Schematic diagram of a section through the horse liver alcohol dehydrogenase dimer. The catalytic zinc atoms are shown, with the inhibitory substrate analogue DMSO and coenzyme molecules indicated. The dimer has two active sites, each composed of parts of both subunits. From the work of Branden and colleagues [123].

Fig. 32. Horse liver alcohol dehydrogenase. The full line shows positions in the apo-enzyme (Fig. 30) and the broken line shows positions in the ternary complex with NADH and dimethyl sulphoxide (Fig. 31). This figure therefore illustrates the movement of active site residues that occurs when the coenzyme and substrate analogue bind. Stereo drawing from the work of Branden and colleagues. 

Complementary structures of biological materials, especially those of proteins, often result in specific recognitions and various types of biological affinity. These include many pairs of substances, such as enzyme-inhibitor, enzyme-substrate (analogue), enzyme-coenzyme, hormone-receptor, and antigen-antibody, as summarized in Table 11.2. Thus, bioaffinity represents a useful approach to separating specific biological materials. 

The observation of MCM-catalyzed hydrogen exchange between substrates and C5 of adenosylcobalamin predated the earliest evidence of radicals in coenzyme Bi2-dependent reactions. Early evidence for the participation of free radicals included the observation of a breakdown in stereochemical specificity in the reaction of the substrate analogue ethylmalonyl-CoA. The weakness of the Co-C5 bond and observation of... 

These products are unable to serve as substrate for glutamyl transfer and are excreted into the culture medium by E. coli. However, products of this type have also been reported more recently to interfere with folate-mediated metabolism. Moreover, the consumption of the dihydropteroate synthase substrate by reaction with the sulfonamide-type substrate analogue may contribute to overall folate-coenzyme depletion. 

Three crystal structures of DD [20,217,219] and two of GD [215,220] have been studied, confirming the base-on nature of the boimd corrinoid. Analysis of the crystal structure of DD reconstituted with the coenzyme B12 analogue 5-adeninyl-pentyl-cobalamin (53) [217] helped identify an adenine-binding pocket in the substrate-binding a-subunit. The observed mode of adenine binding allowed the inference of a build-up of strain in the bound adenosyl-cobamide cofactor and activation towards homolysis of the Co - C bond. 

The ligand to be immobilized can be an inhibitor, a substrate, substrate analogue, coenzyme, or any other biomolecule with an affinity for a specific site (active site, allosteric site, membrane-binding site, etc) on the protein to be purified. Such biomolecules are usually small (mol wt 500), although macromolecules have been successfully employed, eg, with the purification of soybean trypsin inhibitor on immobilized trypsin as a bioselective adsorbent. The precise t5 e of ligand for any purification is dictated by the nature of the enzyme and the aim of the investigation. 

Although, favorable factors are present, the system prefers to remain aromatic. Hence, the formation of NADH in the enzymatic system could be driven by conformational changes that shift the equilibrium toward the nonaromatic species. However, in 1978, a German group (276) observed an intramolecular hydride transfer in the presence of pig heart lactate dehydrogenase using a coenzyme-substrate covalent analogue composed of lactate and NAD+. 

The substrate analogue ethylmalonyl coenzyme A has been used to obtain further information concerning the mechanism of the methylmalonyl-coenzyme A mutase reaction. ... 

Antimetabolites are analogues of normal DNA components or of coenzymes involved in nucleic acid synthesis. They get incorporated or competitively inhibit utilization of normal substrate to form dysfunctional nucleic acid molecules. 

A similarity between the location of zinc(n) in yeast alcohol dehydrogenase (YADH) and that of the metal in LADH has been established.240 NADH and substrate proton relaxation rates using the paramagnetic iodoacetamide analogue complex of YADH show the coenzyme nicotinamide moiety to be situated ca. 7 A from the zinc ion. This is virtually identical with the position of the metal in LADH determined by X-ray crystallography.241 The substrate resides between the NADH and the metal ion, i.e. it is co-ordinated to the zinc. 

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