Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B₁₂ Catalysis

Abstract

The crystal structures of the B -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.

Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme

“…In “base-on” enzymes, the lower ligand base coordinates the central cobalt ion of the cobamide, as drawn in Fig. 1 (53–55). Because the lower ligand is part of the catalytic center of the enzyme, lower ligand structure can influence catalysis through a variety of mechanisms (56–58), and cobamides unable to form an intramolecular coordinate bond are catalytically inactive in base-on enzymes (59, 60).…”

Glycerol as a Substrate and Inactivator of Coenzyme B12‐Dependent Diol Dehydratase

“…[28] Very recently, a crystal structure of B 12 -dDDH with AdoCbl and (S)-PDO has been obtained (PDB code: 5YRT). [29] It is notable that the orientation of 5'-deoxyadenosine is such that H-atom abstraction from either the C1 or C3 atoms of the substrate seems possible, and suggests that an analogous orientation of GOL is possible in this enzyme. We have therefore investigated the possibility of H-atom abstraction from C3 of GOL within B 12 -dDDH and its potential implication for suicide inactivation of this enzyme.…”

“…To validate our structural models obtained from the 3AUJ structure, we compared the average structure obtained from our 2 ns production runs of the system containing (S)-PDO with the recently published crystal structure 5YRV. [29] Of particular interest was the interatomic distances between the C5' carbon of the 5'-deoxyadenosyl radical (Ado * ) and atoms C1 and C3 of the substrate (S)-PDO within 5YRV (Supporting Information, Figure S1).…”

“…Based on research pioneered by Warshel and co-workers, [42][43][44][45] ONIOM calculations [46] were performed to characterize the reaction profiles and possible inactivation mechanisms of three equilibrated model systems: two B 12 -dDDH derived from the crystal structure 5YRV [29] with substrates pro(S)-GOL and (S)-PDO, and B 12 -iGDH derived from the crystal structure 1R9D [10] with substrate pro(S)-GOL.…”

Cofactor selectivity in methylmalonyl-CoA mutase, a model cobamide-dependent enzyme

“…The effect of lower ligand structure on the biochemistry of cobamide-dependent enzymes has been studied to a limited extent. In "base-on" enzymes, the lower ligand base coordinates the central cobalt ion of the cobamide, as drawn in Figure 1 (Larsson et al, 2010;Shibata et al, 2018;Yamanishi et al, 2002). Because the lower ligand is part of the catalytic center of the enzyme, lower ligand structure can influence catalysis through a variety of mechanisms (Brown, 2006;Conrad et al, 2015;Kozlowski and Zgierski, 2004), and cobamides unable to form an intramolecular coordinate bond are catalytically inactive in base-on enzymes (Poppe et al, 2000;Poppe et al, 1997).…”