Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases.
The members of the mechanistically diverse enolase superfamily catalyze different overall reactions by using a common catalytic strategy and structural scaffold. In the muconate lactonizing enzyme (MLE) subgroup of the superfamily, abstraction of a proton adjacent to a carboxylate group initiates reactions, including cycloisomerization (MLE), dehydration [o-succinylbenzoate synthase (OSBS)], and 1,1-proton transfer (catalyzed by an OSBS that also catalyzes a promiscuous N-acylamino acid racemase reaction). The realization that a member of the MLE subgroup could catalyze a 1,1-proton transfer reaction, albeit poorly, led to a search for other enzymes which might catalyze a 1,1-proton transfer as their physiological reaction. YcjG from Escherichia coli and YkfB from Bacillus subtilis, proteins of previously unknown function, were discovered to be L-Ala-D/L-Glu epimerases, although they also catalyze the epimerization of other dipeptides. The values of k(cat)/K(M) for L-Ala-D/L-Glu for both proteins are approximately 10(4) M(-1) s(-1). The genomic context and the substrate specificity of both YcjG and YkfB suggest roles in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Homologues possessing L-Ala-D/L-Glu epimerase activity have been identified in at least two other organisms.
Schmidt
D M
DM
Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, USA.
Hubbard
B K
BK
Gerlt
J A
JA
D000411:Alanine Racemase / Q000737:chemistry / Q000235:genetics; D000591:Amino Acid Isomerases / Q000737:chemistry* / Q000235:genetics; D000595:Amino Acid Sequence; D000626:Aminopeptidases / Q000737:chemistry; D001412:Bacillus subtilis / Q000201:enzymology* / Q000235:genetics; D004151:Dipeptides / Q000737:chemistry; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D019753:Intramolecular Lyases / Q000737:chemistry* / Q000235:genetics; D007700:Kinetics; D008969:Molecular Sequence Data; D010751:Phosphopyruvate Hydratase / Q000737:chemistry* / Q000235:genetics; D019998:Racemases and Epimerases / Q000737:chemistry* / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000737:chemistry
D004151:Dipeptides; D000626:Aminopeptidases; D012697:Serine Endopeptidases; D010751:Phosphopyruvate Hydratase; D019998:Racemases and Epimerases; D000591:Amino Acid Isomerases; D000411:Alanine Racemase; C062292:glutamate racemase; C021540:mandelate racemase; D019753:Intramolecular Lyases; C021811:muconate cycloisomerase