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PDBsum entry 1req
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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How coenzyme b12 radicals are generated: the crystal structure of methylmalonyl-Coenzyme a mutase at 2 a resolution.
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Authors
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F.Mancia,
N.H.Keep,
A.Nakagawa,
P.F.Leadlay,
S.Mcsweeney,
B.Rasmussen,
P.Bösecke,
O.Diat,
P.R.Evans.
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Ref.
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Structure, 1996,
4,
339-350.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 2.
Figure 2. Part of the electron density map at 3 å
resolution that was used to build the model, showing the β
sheet of the C-terminal domain of the α chain, with the refined
model superimposed. Figure 2. Part of the electron density
map at 3 å resolution that was used to build the model,
showing the β sheet of the C-terminal domain of the α chain,
with the refined model superimposed.
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Figure 7.
Figure 7. Schematic representation of ligand binding. (a) The
interactions between protein and coenzyme B[12]. The hydrophobic
pocket for the dimethylbenzimidazole is lined by residues
IleA617, TyrA705, GlyA685 and SerA655: this last forms a
hydrogen bond to the N3B nitrogen atom of the base, which is the
atom that coordinates the cobalt atom in the free coenzyme.
LeuA657 stacks against HisA610, the residue that coordinates the
cobalt, and forms hydrophobic interactions with the beginning
of the pseudo-nucleotide tail (C56) and with the C20 methyl
group of the corrin. (b) The interactions between protein and
desulpho-CoA. TyrA75 stacks on the adenine ring. Note that
ArgB45 is the only interaction between the β chain and the
substrate. CoA would have an additional thiol group attached to
the left-hand end. Figure 7. Schematic representation of
ligand binding. (a) The interactions between protein and
coenzyme B[12]. The hydrophobic pocket for the
dimethylbenzimidazole is lined by residues IleA617, TyrA705,
GlyA685 and SerA655: this last forms a hydrogen bond to the N3B
nitrogen atom of the base, which is the atom that coordinates
the cobalt atom in the free coenzyme. LeuA657 stacks against
HisA610, the residue that coordinates the cobalt, and forms
hydrophobic interactions with the beginning of the
pseudo-nucleotide tail (C56) and with the C20 methyl group of
the corrin. (b) The interactions between protein and
desulpho-CoA. TyrA75 stacks on the adenine ring. Note that
ArgB45 is the only interaction between the β chain and the
substrate. CoA would have an additional thiol group attached to
the left-hand end.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1996,
4,
339-350)
copyright 1996.
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Secondary reference #1
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Title
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Adenosylcobalamin-Dependent methylmalonyl-Coa mutase from propionibacterium shermanii. Active holoenzyme produced from escherichia coli.
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Authors
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N.Mckie,
N.H.Keep,
M.L.Patchett,
P.F.Leadlay.
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Ref.
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Biochem J, 1990,
269,
293-298.
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PubMed id
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