X-Ray Snapshots Of A Pyridoxal Enzyme: A Catalytic Mechanism Involving Concerted [1,5]-Hydrogen Sigmatropy In Methionine Gamma-Lyase

Pyridoxal 5'-phosphate (PLP)-enzymes are essentially involved in amino acid and amine metabolism of a wide variety of organisms. Despite their extensive biochemical studies, there are little evidence and structural data to comprehensively elaborate the catalytic mechanism. We obtained X-ray snapshots of l-methionine gamma-lyase from Entamoeba histolytica (EhMGL), a PLP-enzyme catalyzing the gamma-elimination reaction of methionine. Here, we suggest a catalytic mechanism of EhMGL by using the X-ray snapshots covering all stages of this multistep catalysis reaction. Initial formation of a Michaelis complex is followed by the migration of double bond from the C4'= N alpha-C alpha moiety in an intermediate PLP-methionine imine to C4'-N alpha=C alpha in pyridoxamine 5'-phosphate (PMP)-alpha,beta-dehydromethionine imine without intervention of a putative quinonoid intermediate. The enzyme can facilitate the subsequent gamma- elimination of methanethiol by the possible general acid-base catalysis of Tyr108 for the E1cB mechanism, enabling to form the ene-imine C4'-N alpha=C alpha-C beta N=C gamma structure with the s-cis conformation, which is prerequisite for the non-enzymatic symmetry-allowed suprafacial [1,5]-hydrogen shift to complete the catalytic cycle by releasing alpha-ketobutyrate. The mechanism based on the X-ray snapshots is consistent with the reactivity of MGL toward methionine analogues. The generality of such a mechanism involving non-enzymatic concerted reaction in other PLP enzymes is discussed.