PDBsum entry 1cb7

Isomerase

PDB id: 1cb7

Contents

Protein chains

137 a.a. *

483 a.a. *

Ligands

COB ×2

TAR ×2

Waters ×1013

* Residue conservation analysis

PDB id:

1cb7

Name:

Isomerase

Title:

Glutamate mutase from clostridium cochlearium reconstituted with methyl-cobalamin

Structure:

Protein (glutamate mutase). Chain: a, c. Engineered: yes. Other_details: chains a, c, b, d form heterotetramer which is the biological unit.. Protein (glutamate mutase). Chain: b, d. Engineered: yes. Other_details: complexed with co-methylcobalamin

Source:

Clostridium cochlearium. Organism_taxid: 1494. Atcc: dsm 1285. Collection: dsm 1285. Gene: glms. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: glme.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.166 R-free: 0.219

Authors:

K.Gruber,R.Reitzer,C.Kratky

Key ref:

R.Reitzer et al. (1999). Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights. Structure, 7, 891-902. PubMed id: 10467146 DOI: 10.1016/S0969-2126(99)80116-6

Date:

02-Mar-99 Release date: 28-Feb-00

Protein chains

P80078  (GMSS_CLOCO) -  Glutamate mutase sigma subunit from Clostridium cochlearium

Seq: 137 a.a.

Struc: 137 a.a.*

Protein chains

P80077  (GLME_CLOCO) -  Glutamate mutase epsilon subunit from Clostridium cochlearium

Seq: 483 a.a.

Struc: 483 a.a.*

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

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.5.4.99.1 - methylaspartate mutase.
• Reaction: (2S,3S)-3-methyl-L-aspartate = L-glutamate

(2S,3S)-3-methyl-L-aspartate = L-glutamate (Bound ligand (Het Group name = TAR) matches with 42.86% similarity)

• Cofactor: Cob(II)alamin

Cob(II)alamin (Bound ligand (Het Group name = COB) matches with 84.85% similarity)

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

Added reference

DOI no: 10.1016/S0969-2126(99)80116-6

Structure 7:891-902 (1999)

PubMed id: 10467146

Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights.

R.Reitzer, K.Gruber, G.Jogl, U.G.Wagner, H.Bothe, W.Buckel, C.Kratky.

ABSTRACT

BACKGROUND: Glutamate mutase (Glm) equilibrates (S)-glutamate with (2S,3S)-3-methylaspartate. Catalysis proceeds with the homolytic cleavage of the organometallic bond of the cofactor to yield a 5'-desoxyadenosyl radical. This radical then abstracts a hydrogen atom from the protein-bound substrate to initiate the rearrangement reaction. Glm from Clostridium cochlearium is a heterotetrameric molecule consisting of two sigma and two epsilon polypeptide chains. RESULTS: We have determined the crystal structures of inactive recombinant Glm reconstituted with either cyanocobalamin or methylcobalamin. The molecule shows close similarity to the structure of methylmalonyl CoA mutase (MCM), despite poor sequence similarity between its catalytic epsilon subunit and the corresponding TIM-barrel domain of MCM. Each of the two independent B12 cofactor molecules is associated with a substrate-binding site, which was found to be occupied by a (2S,3S)-tartrate ion. A 1:1 mixture of cofactors with cobalt in oxidation states II and III was observed in both crystal structures of inactive Glm. CONCLUSIONS: The long axial cobalt-nitrogen bond first observed in the structure of MCM appears to result from a contribution of the species without upper ligand. The tight binding of the tartrate ion conforms to the requirements of tight control of the reactive intermediates and suggests how the enzyme might use the substrate-binding energy to initiate cleavage of the cobalt-carbon bond. The cofactor does not appear to have a participating role during the radical rearrangement reaction.

Selected figure(s)

Figure 5.
Figure 5. Ribbon representation of the epsilon, Greek [2]s[2](B[12])[2] tartrate[2] heterotetramer of Glm, viewed down the noncrystallographic dyad. The two epsilon, Greek subunits are coloured in red and green and the two s subunits are in yellow and blue. The B[12] cofactors are in cyan and the tartrate ions in magenta.

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 891-902) copyright 1999.

Figure was selected by an automated process.