Coenzyme dependent enzymes

There is one exception to the rule that requires bulky hydrophobic residues to fill the interior of eight-stranded a/p barrels in order to form a tightly packed hydrophobic core. The coenzyme Biz-dependent enzyme methylmalonyl-coenzyme A mutase, the x-ray structure of which was determined by Phil Evans and colleagues at the MRC Laboratory of Molecular... 

Johnson EF, B Mukhopadhyay (2005) A new type of sulfite reductase, a novel coenzyme F420 -dependent enzyme, from the methanarchaeon Methanocaldocccus jannaschii. J Biol Client 280 38776-38786. 

Boyd JM, A Ellsworth, SA Ensign (2006) Characterization of 2-bromoethanesulfonate as a selective inhibitor of the coenzyme M-dependent pathway and enzymes of bacterial aliphatic epoxide metabolism. J Bacteriol 188 8062-8069. 

The assay methods reported in the literature vary with respect to the use of methylene blue or another dye, and to the coenzyme used, depending on enzyme source, etc. 

Significant advances have been made in the preparation of discrete macromolecules that include both coenzyme function and a defined polypeptide or protein architecture. Preliminary, but promising, functional studies have been carried out and assay methods developed. While in many cases rather modest effects have been observed, what is significant is that the methodology exists to prepare, characterize, and study defined macromolecular constructs. With new information becoming available on co enzyme-dependent protein catalysts from structural biology and mechanistic enzymology, it should be possible to more fully exploit the remarkable breadth of coenzyme reactivity in tailored synthetic systems. 

Enzymes dependent on folic acid as coenzyme include participants in the synthesis of thymine, an essential component of DNA, and methionine, a common amino acid in proteins, among other important metabolites. A deficiency of folic acid results in the disease megaloblastic anemia. 

D. M. Smith, S. D. Wetmore, and L. Radom, Theoretical Studies of Coenzyme-Bi2-Dependent Carbon-Skeleton Rearrangements, in Theoretical Biochemistry—Processes and Properties of Biological Systems, L. A. Ericksson, Ed., Elsevier, Amsterdam, The Netherlands, 2001, pp. 183-214. Electronic structure calculations are applied to the understanding and prediction of how enzymes can lower the barriers to the 1,2-shifts in radicals that occur in reactions catalyzed by B12. 

Table I lists isomorphous replacements for various metalloproteins. Consider zinc enzymes, most of which contain the metal ion firmly bound. The diamagnetic, colorless zinc atom contributes very little to those physical properties that can be used to study the enzymes. Thus it has become conventional to replace this metal by a different metal that has the required physical properties (see below) and as far as is possible maintains the same activity. Although this aim may be achieved to a high degree of approximation [e.g., replacement of zinc by cobalt(II)], no such replacement is ever exact. This stresses the extreme degree of biological specificity. The action of an enzyme depends precisely on the exact metal it uses, stressing again the peculiarity of biological action associated with the idiosyncratic nature of active sites. (The entatic state of the metal ion is an essential part of this peculiarity.) Despite this specificity, the replacement method has provided a wealth of information about proteins that could not have been obtained by other methods. Clearly, there will often be a compromise in the choice of replacement. Even isomorphous replacement that should retain structure will not necessarily retain activity at all. However, it has become clear that substitutions can be made for structural studies where the substituted protein is inactive (e.g., in the copper proteins and the iron-sulfur proteins). It is also possible to substitute into metal coenzymes. Many studies have been reported of the...

D. 4. Pumping Ions with the Help of Biotin Thiamin Diphosphate 735. .. Table 14-2 Enzymes Dependent upon Thiamin Diphosphate as a Coenzyme... 

Enzymes Dependent upon Thiamin Diphosphate as a Coenzyme... 

Unfortunately, the one x-ray structure of a coenzyme B -dependent enzyme reported has disorder problems and has a mixture of forms of the cofactor thus, it is difficult to discern well the role of the protein [33]. The evidence that protein-cofactor contacts are important in the activation process is limited almost exclusively to a few of the coenzyme B 12-dependent enzymes. This evidence will be discussed later. 

The preceding qualitative picture requires further investigation of both the energetics and structural changes in models and cobalamins. However, if it represents a reasonable approximation of the interrelationships among structure, coordination number, and axial bond strengths, then the intermediacy of 5-coordinate ComR species in the enzymatic process involving Co" and radical chemistry of coenzyme B -dependent enzymes appears unlikely. 

The specific interaction of Cibacron Blue and its derivatives to dinucleotides, mainly to NAD, NADP and ATP offers the possibility of purifing all enzymes which are dependent on these coenzymes. According to Mosbach < - > there are 163 enzymes requiring NAD, 141 enzymes requiring NADP, about 40 enzymes requiring NADP or NAD and 225 enzymes dependent on ATP. Besides these specific interactions non-specific interactions of Cibacron Blue and its derivatives with. proteins can also be applied for separation purposes. The non-specific interaction of Cibacron Blue with human serum albumin, for instance, enables albumin to be removed from transferrin, ceruloplasmin or other plasma proteins in order to purify human... 

Reitzer, R., Gruber, K., Jogl, G., Wagner, U. G., Bothe, H., Buckel, W., and Kratky, C. 1999, Structure of coenzyme Bj2 dependent enzyme glutamate mutase from Clostridium cochlearium. Structure 7 8919902. 

About 10 coenzyme B -dependent enzymes are now known (reviewed in References 13,14, and 76 see Table 1) four carbon skeleton mutases (methylmalonyl-CoA mutase (MMCM), glutamate mutase (GM), methylene glu-tarate mutase (MGM), isobutyryl-CoA mutase (ICM) ), diol dehydratase (DD), glycerol dehydratase, ethanol-amine anunonia lyase (EAL), two amino mutases, and Bi2-dependent ribonucleotide reductase. The coenzyme Bi2-dependent enzymes are unevenly distributed in the living world, and MMCM is the only enzyme that is also indispensable in human metabolism. ... 

The known coenzyme Bi2-dependent enzymes all perform chemical transformations in enzymatic radical reactions that are difficult to achieve by typical organic reactions. Homolytic cleavage of the Co bond of the protein-bound coenzyme B12 (3) to a 5 -deoxy-5 -adenosyl radical (9) and cob(n)alamin (5) is the entry to reversible H-abstraction reactions involving the 5 -position of the radical (9). Indeed, homolysis of the Co bond is the thermally most easily achieved transformation of coenzyme B12 (3) in neutral aqueous solution (with a homolytic (Co-C)-BDE of about 30 kcal mol ). However, to be relevant for the observed rates of catalysis by the coenzyme B12-dependent enzymes, the homolysis of the Co-C bond of the protein-bound coenzyme (3) needs to be accelerated by a factor of about 10 , in the presence of a substrate. Coenzyme B12 might then be considered, first of aU, to be a structurally sophisticated, reversible source for an alkyl radical, whose Co bond is labihzed in the protein-bound state (Figure 8), and the first major task of the... 

The coenzyme Bi2-dependent enzymes all rely npon the reactivity of bonnd organic radicals that are formed (directly or indirectly) by a H-atom abstraction by the 5 -deoxy-5 -adenosyl radical (9). In these enzymatic reactions, the radical (9) is the established reactive partner in the proper enzymatic radical reaction, so that AdoCbl (3) shonld be looked at as a precatalyst (or catalyst precnrsor ). Tight control of the reactivity and correct mntnal orientation... 

Table 1 Classification of Coenzyme B12-dependent Radical Enzymes ...

This enzyme s role in humans is to assist the detoxification of propionate derived from the degradation of the amino acids methionine, threonine, valine, and isoleucine. Propionyl-CoA is carboxylated to (5 )-methylmalonyl-CoA, which is epimerized to the (i )-isomer. Coenzyme Bi2-dependent methylmalonyl-CoA mutase isomerizes the latter to succinyl-CoA (Fig. 2), which enters the Krebs cycle. Methylmalonyl-CoA mutase was the first coenzyme B -dependent enzyme to be characterized crystallographically (by Philip Evans and Peter Leadlay). A mechanism for the catalytic reaction based on ab initio molecular orbital calculations invoked a partial protonation of the oxygen atom of the substrate thioester carbonyl group that facilitated formation of an oxycyclopropyl intermediate, which connects the substrate-derived and product-related radicals (14). The partial protonation was supposed to be provided by the hydrogen bonding of this carbonyl to His 244, which was inferred from the crystal structure of the protein. The ability of the substrate and product radicals to interconvert even in the absence of the enzyme was demonstrated by model studies (15). 

Bnckel W, Golding BT. Glntamate and 2-methyleneglntarate mntase from microbial cnriosities to paradigms for coenzyme Bi2-dependent enzymes. Chem. Soc. Rev. 1996 26 329-337. 

---