title: Large-scale domain conformational change is coupled to the activation of the Co-C bond in the B12-dependent enzyme ornithine 4,5-aminomutase: a computational study.
abstract: We present here an energetic and atomistic description of how D-ornithine 4,5-aminomutase (OAM), an adenosylcobalamin (AdoCbl; coenzyme B(12))-dependent isomerase, employs a large-scale protein domain conformational change to orchestrate the homolytic rupture of the Co-C bond. Our results suggest that in going from the open form (catalytically inactive) to the closed form (catalytically active), the Rossmann domain of OAM effectively approaches the active site as a rigid body. It undergoes a combination of a ~52° rotation and a ~14 Å translation to bring AdoCbl-initially positioned ~25 Å away-into the active-site cavity. This process is coupled to repositioning of the Ado moiety of AdoCbl from the eastern conformation to the northern conformation. Combined quantum mechanics and molecular mechanics calculations further indicate that in the open form, the protein environment does not impact significantly on the Co-C bond homolytic rupture, rendering it unusually stable, and thus catalytically inactive. Upon formation of the closed form, the Co-C bond is activated through the synergy of steric and electrostatic effects arising from tighter interactions with the surrounding enzyme. The more pronounced effect of the protein in the closed form gives rise to an elongated Co-C bond (by 0.03 Å), puckering of the ribose and increased "strain" energy on the Ado group and to a lesser extent the corrin ring. Our computational studies reveal novel strategies employed by AdoCbl-dependent enzymes in the control of radical catalysis.
authors.affiliation: Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom. j.pang@gre.ac.uk
authors.forename: Jiayun
authors.initials: J
authors.lastname: Pang
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Keiji
authors.initials: K
authors.lastname: Morokuma
authors.forename: Nigel S
authors.initials: NS
authors.lastname: Scrutton
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sutcliffe
mesh_terms: D002244:Carbon / Q000737:chemistry*; D003035:Cobalt / Q000737:chemistry*; D003038:Cobamides / Q000737:chemistry*; D019751:Intramolecular Transferases / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D013237:Stereoisomerism
chemical_list: D003038:Cobamides; D003035:Cobalt; D002244:Carbon; D019751:Intramolecular Transferases; C021913:ornithine 5,4-aminomutase; C000913:cobamamide