How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A resolution.
BACKGROUND
The enzyme methylmalonyl-coenzyme A (CoA) mutase, an alphabeta heterodimer of 150 kDa, is a member of a class of enzymes that uses coenzyme B12 (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 A resolution of methylmalonyl-CoA mutase from Propionibacterium shermanii in complex with coenzyme B12 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 B12-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 (beta/alpha)8 TIM barrel domain.


CONCLUSIONS
The histidine-cobalt distance is very long (2.5 A compared with 1.95-2.2 A 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.
Mancia
F
F
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
Keep
N H
NH
Nakagawa
A
A
Leadlay
P F
PF
McSweeney
S
S
Rasmussen
B
B
Bösecke
P
P
Diat
O
O
Evans
P R
PR
D001665:Binding Sites; D003038:Cobamides / Q000378:metabolism*; D003460:Crystallization; D018360:Crystallography, X-Ray; D005609:Free Radicals / Q000378:metabolism; D008024:Ligands; D008765:Methylmalonyl-CoA Mutase / Q000737:chemistry*; D008958:Models, Molecular; D011424:Propionibacterium / Q000201:enzymology; D017433:Protein Structure, Secondary; D013379:Substrate Specificity
D003038:Cobamides; D005609:Free Radicals; D008024:Ligands; D008765:Methylmalonyl-CoA Mutase; C000913:cobamamide