Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift

Abstract

Malyl CoA lyase (MCL) is an Mg 2+ dependent enzyme that catalyzes the reversible cleavage of (2S) 4 malyl CoA to yield acetyl CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase like family and are involved in the assimilation of one and two carbon compounds. Here, the 1.56 Å resolution X ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg 2+ is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl CoA lyase complexed with Mg 2+, oxalate and CoA allows a detailed analysis of the domain motion of the enzyme caused by substrate binding. Alignment of the structures shows that a simple hinge motion centered on the conserved residues Phe268 and Thr269 moves the C terminal domain by about 30° relative to the rest of the molecule. This domain motion positions a conserved aspartate residue located in the C terminal domain in the active site of the adjacent monomer, which may serve as a general acid/base in the catalytic mechanism.