Crystal structure of methylmalonyl-coenzyme A epimerase from P-shermanii: a novel enzymatic function on an ancient metal binding scaffold

Background: Methylmalonyl-CoA epimerase (MMCE) is an essential enzyme in th e breakdown of odd-numbered fatty acids and of the amino acids valine, isol eucine, and methionine. Present in many bacteria and in animals, it catalyz es the conversion of (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, the substrate for the B-12-dependent enzyme, methylmalonyl-CoA mutase. Defects in this pathway can result in severe acidosis and cause damage to the centr al nervous system in humans. Results: The crystal structure of MMCE from Propionibacterium shermanii has been determined at 2.0 Angstrom resolution. The MMCE monomer is folded int o two tandem beta alpha beta beta beta modules that pack edge-to-edge to ge nerate an 8-stranded beta sheet. Two monomers then pack back-to-back to cre ate a tightly associated dimer. In each monomer, the beta sheet curves arou nd to create a deep cleft, in the floor of which His12, Gln65, His91, and G lu141 provide a binding site for a divalent metal ion, as shown by the bind ing of Co2+. Modeling 2-methylmalonate into the active site identifies two glutamate residues as the likely essential bases for the epimerization reac tion. Conclusions: The beta alpha beta beta beta modules of MMCE correspond with those found in several other proteins, including bleomycin resistance prote in, glyoxalase I, and a family of extradiol dioxygenases. Differences in co nnectivity are consistent with the evolution of these very different protei ns from a common precursor by mechanisms of gene duplication and domain swa pping. The metal binding residues also align precisely, and striking struct ural similarities between MMCE and glyoxalase I suggest common mechanisms i n their respective epimerization and isomerization reactions.