| Abstract
| - The 3-keto-l-gulonate 6-phosphate decarboxylase (KGPDC) encoded by the ulaD gene in theEscherichia coli genome [Yew, W. S., and Gerlt, J. A. (2002) J. Bacteriol.184, 302−306] and orotidine5‘-monophosphate decarboxylase (OMPDC) are homologous (derived from a common ancestor) but catalyzedifferent reactions. The metal-independent decarboxylation reaction catalyzed by OMPDC avoids theformation of a vinyl anion intermediate; the Mg2+-dependent decarboxylation reaction catalyzed by KGPDCinvolves the formation of an enediolate anion intermediate. Based on the available structures of OMPDC,a sequence alignment allows the predictions that (1) KGPDC is a dimer of (β/α)8-barrels, with the activesites located at the dimer interface; (2) KGPDC and OMPDC share an aspartate residue at the end of thefirst β-strand and an Asp-x-Lys-x-x-Asp motif at the end of the third β-strand with OMPDC; but (3)KGPDC has a Glu instead of a Lys at the end of the second β-strand. The structure of KGPDC has beendetermined in the presence of Mg2+ and the substrate analogue l-gulonate 6-phosphate and confirmsthese predictions. The carboxylate functional groups at the ends of the first, second, and third β-strandsin KGPDC are ligands of the Mg2+; in OMPDC, the homologues of these residues participate in a hydrogen-bonded network that facilitates the decarboxylation reaction. The 3-OH group of the substrate analogueis coordinated to the Mg2+, supporting the hypothesis that the mechanism of the decarboxylation catalyzedby KGPDC involves stabilization of an enediolate anion intermediate. These structural studies establishthe existence of the OMPDC “suprafamily,” in which members catalyze reactions that occur in differentmetabolic pathways and share no mechanistic relationship. The existence of this suprafamily demonstratesthat divergent evolution can be opportunistic, conscripting active site features of a progenitor to catalyzeunrelated functions. Accordingly, sequence or structure homology alone cannot be used to infer the functionsof new proteins discovered in genome projects.
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