Co⁺–H interaction inspired alternate coordination geometries of biologically important cob(I)alamin: possible structural and mechanistic consequences for methyltransferases

Abstract

A detailed computational analysis employing density functional theory (DFT), atoms in molecules, and quantum mechanics/molecular mechanics (QM/MM) tools has been performed to investigate the primary coordination environment of cob(I)alamin (Co⁺Cbx), which is a ubiquitous B₁₂ intermediate in methyltransferases and ATP:corrinoid adenosyltransferases. The DFT calculations suggest that the simplified (Co⁺Cbl) as well as the complete (Co⁺Cbi) complexes can adapt to the square pyramidal or octahedral coordination geometry owing to the unconventional H-bonding between the Co⁺ ion and its axial ligands. These Co⁺–H bonds contain appreciable amounts of electrostatic, charge transfer, long-range correlation, and dispersion components. The computed reduction potentials of the Co²⁺/Co⁺ couple imply that the Co⁺–H(H₂O) interaction causes a greater anodic shift [5–98 mV vs. the normal hydrogen electrode (NHE) in chloroform solvent] than the analogous Co⁺–H(imidazole) interaction (1 mV vs. NHE) in the reduction potential of the Co²⁺/Co⁺ couple. This may explain why a β-axial H₂O ligand has specifically been found in the active sites of certain methyltransferases. The QM/MM analysis of methionine synthase bound Co⁺Cbx (Protein Data Bank ID 1BMT, resolution 3.0 Å) indicates that the enzyme-bound Co⁺Cbx can also form a Co⁺–H bond, but can only exist in square pyramidal form because of the steric constraints imposed by the cellular environment. The present calculations thus support a recently proposed alternate mechanism for the enzyme-bound Co²⁺/Co⁺ reduction that involves the conversion of square pyramidal Co²⁺Cbx into square pyramidal Co⁺Cbx (Kumar and Kozlowski in Angew. Chem. Int. Ed. 50:8702–8705, 2011).