Racemases structure

G. L. Kenyon, J. A. Gerlt, G. A. Petsko, and J. W. Kozarich, Mandelate racemase structure-function studies of a pseudo-symmetric enzyme, Acc. Chem. Res. 1995, 28, 178-186. 

Isotnerases. These catalyse the structural or geometric changes within a molecule. The division includes racemases, epimerases, cis-rran -isomerases, lautomerases and mulases. 

Neidhart, D.J., et al. Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous. Nature 347 ... 

The tertiary structure of glutamate racemase has already been resolved and it has also been shown that a substrate analog glutamine binds between two cysteine residues. These data enabled us to predict that the new proton-donating amino acid residue should be introduced at position 74 instead of Gly for the inversion of enantioselectivity of the decarboxylation reaction. 

Mandelate racemase, another pertinent example, catalyzes the kinetically and thermodynamically unfavorable a-carbon proton abstraction. Bearne and Wolfenden measured deuterium incorporation rates into the a-posi-tion of mandelate and the rate of (i )-mandelate racemi-zation upon incubation at elevated temperatures. From an Arrhenius plot, they obtained a for racemization and deuterium exchange rate was estimated to be around 35 kcal/mol at 25°C under neutral conditions. The magnitude of the latter indicated mandelate racemase achieves the remarkable rate enhancement of 1.7 X 10, and a level of transition state affinity (K x = 2 X 10 M). These investigators also estimated the effective concentrations of the catalytic side chains in the native protein for Lys-166, the effective concentration was 622 M for His-297, they obtained a value 3 X 10 M and for Glu-317, the value was 3 X 10 M. The authors state that their observations are consistent with the idea that general acid-general base catalysis is efficient mode of catalysis when enzyme s structure is optimally complementary with their substrates in the transition-state. See Reference Reaction Catalytic Enhancement... 

LeMagueres, R Im, H. Dvorak, A. Strych, U. Benedik, M. Krause, K. L. Crystal Structure at 1.45 A Resolution of Alanine Racemase from a Pathogenic Bacterium, Pseudomonas aeruginosa, Contains Both Internal and External Aldimine Forms. Biochemistry 2003, 42, 14752-14761. 

T Although D-amino acids do not generally occur in proteins, they do serve some special functions in the structure of bacterial cell walls and peptide antibiotics. Bacterial peptidoglycans (see Fig. 20-23) contain both D-alanine and D-glutamate. D-Amino acids arise directly from the l isomers by the action of amino acid racemases, which have pyridoxal phosphate as cofactor (see Fig. 18-6). Amino acid racemization is uniquely important to bacterial metabolism, and enzymes such as... 

The degradation of mandelic acid by the bacterium Pseudomonas putida (Chapter 25) is initiated by mandalate racemase, another (a/(3)8-barrel protein.101 X-ray structures of bound inhibitors together with modeling suggest that the side chain of Lys 264 is the catalytic base that abstracts the a-H from S-mandelate (Fig. 13-5) and that the catalytic pair of His 297 and Asp 270 acts as proton donor, or, in the reverse direction, as catalytic... 

Another enzyme-activated inhibitor is the streptomyces antibiotic D-cycloserine (oxamycin), an antitubercular drug that resembles D-alanine in structure. A potent inhibitor of alanine racemase, it also inhibits die non-PLP, ATP-dependent, D-alanyl-D-alanine synthetase which is needed in the biosynthesis of die peptidoglycan of bacterial cell walls. 

Lack of congruence of sequence and structure with function Common sequence and structure, indeed identity of the protein itself, do not imply a unique function Each pair, o-succinylbenzoate synthase (OSBS)-N-acetylamino acid racemase, and lens crystallin-lactate dehydrogenase, share sequence and structure but differ in function. 

Inhibits the enzymes alanine racemase and D-alanyl-D-alanyl synthetase that are responsible for producing the dipeptide D-alanyl-D-alanine, a precursor of the pentapeptide chain in cell wall formation. It is believed that the rigid structure of the isoxazole ring gives the drug a better chance of binding to the enzyme than the more flexible structure of D-alanine. 

Structure of Thermostable Alanine Racemase of Bacillus stearothermophilus... 

The subunit dissociation is usually accompanied by destruction of the secondary structures when thermolabile proteins are used. The thermostable alanine racemase is very useful for studying the mechanism of subunit dissociation and protein unfolding. 

Faraci and Walsh263 studied the substrate and solvent deuterium isotope effects of the reactions catalyzed by alanine racemases of S. typhimurium (DadB and Air enzymes) and B. stearothermophilus. Although the kinetic constants for all three alanine racemases obey the Haldane equation, i.e., Keq= 1 (this confirms that the enzymes are true racemases), the individual Micaelis-Menten parameters in both directions show marked difference in the binding of each isomer. This suggests a structural asymmetry at the active sites of these enzymes. The asymmetry in the recognition and turnover of substrate enantiomer was also clearly seen in the results of isotope effect experiment with DadB enzyme. In the d-... 

The enolase superfamily story started with the serendipitous discovery that two enzymes catalyzing very different overall reactions, mandelate racemase (MR) and muconate lactonizing enzyme (MLE), had virtually superimposable structures (Neidhart et al., 1990). As shown in Figure 2, MR catalyzes the reversible racemization of mandelate, an aromatic substrate, while MLE catalyzes the equilibration of muconolactone with as, m-muconate. Given the substantial differences in these reactions, it... 

Like MR, NAAAR represents another racemase activity in the enolase superfamily. As would be expected, this enzyme contains machinery for initiation of its chemical reaction by abstraction of the a-proton from either an R- or an S-substrate. Thus, NAAAR possesses the S-specific base motif, KXK, as well an R-specific base, this time a Lys, in contrast to the His/Asp dyad in MR (Fig. 8). For this reason, NAAAR was originally assigned to the MLE subgroup, the structurally characterized member of the superfamily to which it is most similar (29% identical to the MLE I of P. putida) and which also has a Lys residue in the R-specific base position. Unlike any other members of the superfamily, however, NAAAR is a remarkably inefficient enzyme (Ka/Km = 3.7 X 102 M-1 s 1). 

Class 5. Isomerases interconvert isomeric structures by intramolecular rearrangements. They include racemases, epimerases, cis- and trans-isomerases, intramolecular transferases (mutases), and intermolecular lyases. 

While the production of D-amino acids is well established the preparation of L-amino acids is difficult due to the limited selectivity and narrow substrate spectrum of L-hydantoinases. This can be circumvented by employing rather un-selective hydantoinases in combination with very enantioselective L-carbamoyl-ases and carbamoyl racemases [90]. Furthermore, a D-hydantoinase has been genetically modified and converted into a L-hydantoinase. This enzyme can be used on a 100-kg scale for the production of L-tert-leucine [34]. Finally, the fact that the X-ray structure of an L-hydantoinase is known gives hope that side-directed mutagenesis will lead to improved L-hydantoinases [91]. 

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