How coenzyme B 12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 å resolution

Abstract

Background: The enzyme methylmalonyl-coenzyme A (CoA) mutase, an α β heterodimer of 150 kDa, is a member of a class of enzymes that uses coenzyme B 12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA. Results Reported here is the crystal structure at 2 å resolution of methylmalonyl-CoA mutase from Propionibacterium shermanii in complex with coenzyme B 12 and with the partial substrate desulpho-CoA (lacking the succinyl group and the sulphur atom of the substrate). The coenzyme is bound by a domain which shares a similar fold to those of flavodoxin and the B 12-binding domain of methylcobalamin-dependent methionine synthase. The cobalt atom is coordinated, via a long bond, to a histidine from the protein. The partial substrate is bound along the axis of a ( β/ α) 8 TIM barrel domain. Conclusion The histidine–cobalt distance is very long (2.5 å compared with 1.95–2.2 å in free cobalamins), suggesting that the enzyme positions the histidine in order to weaken the metal–carbon bond of the cofactor and favour the formation of the initial radical species. The active site is deeply buried, and the only access to it is through a narrow tunnel along the axis of the TIM barrel domain.