Crystal Structure of Methylmalonyl-Coenzyme A Epimerase from P. shermanii: a Novel Enzymatic Function on an Ancient Metal Binding Scaffold

Abstract

Background: Methylmalonyl-CoA epimerase (MMCE) is an essential enzyme in the breakdown of odd-numbered fatty acids and of the amino acids valine, isoleucine, and methionine. Present in many bacteria and in animals, it catalyzes 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 central nervous system in humans. Results: The crystal structure of MMCE from Propionibacterium shermanii has been determined at 2.0 Å resolution. The MMCE monomer is folded into two tandem βαβββ modules that pack edge-to-edge to generate an 8-stranded β sheet. Two monomers then pack back-to-back to create a tightly associated dimer. In each monomer, the β sheet curves around to create a deep cleft, in the floor of which His12, Gln65, His91, and Glu141 provide a binding site for a divalent metal ion, as shown by the binding of Co 2+. Modeling 2-methylmalonate into the active site identifies two glutamate residues as the likely essential bases for the epimerization reaction. Conclusions: The βαβββ modules of MMCE correspond with those found in several other proteins, including bleomycin resistance protein, glyoxalase I, and a family of extradiol dioxygenases. Differences in connectivity are consistent with the evolution of these very different proteins from a common precursor by mechanisms of gene duplication and domain swapping. The metal binding residues also align precisely, and striking structural similarities between MMCE and glyoxalase I suggest common mechanisms in their respective epimerization and isomerization reactions.