PDBsum entry 1req

Isomerase

PDB id: 1req

Contents

Protein chains

727 a.a. *

619 a.a. *

Ligands

B12 ×2

DCA ×2

GOL ×9

Waters ×1532

* Residue conservation analysis

PDB id:

1req

Name:

Isomerase

Title:

Methylmalonyl-coa mutase

Structure:

Methylmalonyl-coa mutase. Chain: a, c. Engineered: yes. Other_details: chains a and c include coenzyme b12, desulpho-coa, and a glycerol in the active site. B12 is present largely as reduced cob(ii)alamin, or b12r.. Methylmalonyl-coa mutase. Chain: b, d. Engineered: yes.

Source:

Propionibacterium freudenreichii subsp. Shermanii. Organism_taxid: 1752. Strain: ncib 9885. Cell_line: 293. Gene: muta mutb. Expressed in: k38 pgp1-2. Other_details: the 2 genes muta (beta chain) and mutb (alpha chain) are coexpressed from the same plasmid.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.220 R-free: 0.275

Authors:

P.R.Evans,F.Mancia

Key ref:

F.Mancia et al. (1996). How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A resolution. Structure, 4, 339-350. PubMed id: 8805541 DOI: 10.1016/S0969-2126(96)00037-8

Date:

19-Jan-96 Release date: 27-Jan-97

Protein chains

P11653  (MUTB_PROFR) -  Methylmalonyl-CoA mutase large subunit from Propionibacterium freudenreichii subsp. shermanii

Seq: 728 a.a.

Struc: 727 a.a.

Protein chains

P11652  (MUTA_PROFR) -  Methylmalonyl-CoA mutase small subunit from Propionibacterium freudenreichii subsp. shermanii

Seq: 638 a.a.

Struc: 619 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.5.4.99.2 - methylmalonyl-CoA mutase.
• Reaction: (R)-methylmalonyl-CoA = succinyl-CoA

(R)-methylmalonyl-CoA (Bound ligand (Het Group name = DCA) matches with 85.45% similarity) = succinyl-CoA

• Cofactor: Cob(II)alamin

Cob(II)alamin (Bound ligand (Het Group name = B12) matches with 85.71% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0969-2126(96)00037-8

Structure 4:339-350 (1996)

PubMed id: 8805541

How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A resolution.

F.Mancia, N.H.Keep, A.Nakagawa, P.F.Leadlay, S.McSweeney, B.Rasmussen, P.Bösecke, O.Diat, P.R.Evans.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 339-350) copyright 1996.

Figures were selected by an automated process.