PDBsum entry 3bul

Transferase

PDB id: 3bul

Contents

Protein chain

577 a.a. *

Ligands

B12

Waters ×63

* Residue conservation analysis

PDB id:

3bul

Name:

Transferase

Title:

E. Coli i690c/g743c meth c-terminal fragment (649-1227)

Structure:

Methionine synthase. Chain: a. Fragment: c-terminal activation complex (residues 649-1227). Synonym: 5-methyltetrahydrofolate-homocysteine methyltransferase, methionine synthase, vitamin-b12- dependent, ms. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: meth. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.200 R-free: 0.247

Authors:

M.Koutmos,K.A.Pattridge,M.L.Ludwig

Key ref:

S.Datta et al. (2008). A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor. Proc Natl Acad Sci U S A, 105, 4115-4120. PubMed id: 18332423 DOI: 10.1073/pnas.0800329105

Date:

03-Jan-08 Release date: 01-Apr-08

Protein chain

P13009  (METH_ECOLI) -  Methionine synthase from Escherichia coli (strain K12)

Seq: 1227 a.a.

Struc: 577 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.13 - methionine synthase.
• Pathway: Methionine Synthase
• Reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8- tetrahydrofolate + L-methionine
• Cofactor: Cob(II)alamin; Zn(2+)

Cob(II)alamin (Bound ligand (Het Group name = B12) matches with 85.71% similarity) Zn(2+)

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

reference

DOI no: 10.1073/pnas.0800329105

Proc Natl Acad Sci U S A 105:4115-4120 (2008)

PubMed id: 18332423

A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor.

S.Datta, M.Koutmos, K.A.Pattridge, M.L.Ludwig, R.G.Matthews.

ABSTRACT

B(12)-dependent methionine synthase (MetH) from Escherichia coli is a large modular protein that is alternately methylated by methyltetrahydrofolate to form methylcobalamin and demethylated by homocysteine to form cob(I)alamin. Major domain rearrangements are required to allow cobalamin to react with three different substrates: homocysteine, methyltetrahydrofolate, and S-adenosyl-l-methionine (AdoMet). These same rearrangements appear to preclude crystallization of the wild-type enzyme. Disulfide cross-linking was used to lock a C-terminal fragment of the enzyme into a unique conformation. Cysteine point mutations were introduced at Ile-690 and Gly-743. These cysteine residues span the cap and the cobalamin-binding module and form a cross-link that reduces the conformational space accessed by the enzyme, facilitating protein crystallization. Here, we describe an x-ray structure of the mutant fragment in the reactivation conformation; this conformation enables the transfer of a methyl group from AdoMet to the cobalamin cofactor. In the structure, the axial ligand to the cobalamin, His-759, dissociates from the cobalamin and forms intermodular contacts with residues in the AdoMet-binding module. This unanticipated intermodular interaction is expected to play a major role in controlling the distribution of conformers required for the catalytic and the reactivation cycles of the enzyme.

Selected figure(s)

Figure 1.
The catalytic (red) and reactivation (blue) cycles of E. coli MetH. During catalysis the cobalamin cofactor is alternately methylated by CH[3]-H[4]folate and demethylated by Hcy. The cob(I)alamin form of the enzyme is occasionally oxidized to form the inactive cob(II)alamin form. Return of this species to the catalytic cycle involves reduction with electrons derived from reduced flavodoxin and methylation with a methyl group derived from AdoMet.

Figure 6.
Intermodular interactions involving His-759 in the His-off state. Nε2 of His-759 interacts with the AdoMet module directly through a hydrogen bond to Asp-1093 and via a water-mediated hydrogen bond to Glu-1069. Nδ1 of His-759 forms a hydrogen bond with the amide of the propionamide side chain of ring B of the cobalamin (data not shown).

Figures were selected by an automated process.