Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half with AdoHcy bound

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Insights into the reactivation of cobalamin-dependent methionine synthase.

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

(2009) Proc Natl Acad Sci U S A 106: 18527-18532

  • DOI: https://doi.org/10.1073/pnas.0906132106
  • Primary Citation of Related Structures:  
    3IV9, 3IVA

  • PubMed Abstract: 

    Cobalamin-dependent methionine synthase (MetH) is a modular protein that catalyzes the transfer of a methyl group from methyltetrahydrofolate to homocysteine to produce methionine and tetrahydrofolate. The cobalamin cofactor, which serves as both acceptor and donor of the methyl group, is oxidized once every approximately 2,000 catalytic cycles and must be reactivated by the uptake of an electron from reduced flavodoxin and a methyl group from S-adenosyl-L-methionine (AdoMet). Previous structures of a C-terminal fragment of MetH (MetH(CT)) revealed a reactivation conformation that juxtaposes the cobalamin- and AdoMet-binding domains. Here we describe 2 structures of a disulfide stabilized MetH(CT) ((s-s)MetH(CT)) that offer further insight into the reactivation of MetH. The structure of (s-s)MetH(CT) with cob(II)alamin and S-adenosyl-L-homocysteine represents the enzyme in the reactivation step preceding electron transfer from flavodoxin. The structure supports earlier suggestions that the enzyme acts to lower the reduction potential of the Co(II)/Co(I) couple by elongating the bond between the cobalt and its upper axial water ligand, effectively making the cobalt 4-coordinate, and illuminates the role of Tyr-1139 in the stabilization of this 4-coordinate state. The structure of (s-s)MetH(CT) with aquocobalamin may represent a transient state at the end of reactivation as the newly remethylated 5-coordinate methylcobalamin returns to the 6-coordinate state, triggering the rearrangement to a catalytic conformation.

  • Organizational Affiliation

    Department of Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine synthase579Escherichia coliMutation(s): 2 
Gene Names: b4019JW3979metH
Find proteins for P13009 (Escherichia coli (strain K12))
Explore P13009 
Go to UniProtKB:  P13009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13009
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.006α = 90
b = 107.006β = 90
c = 141.185γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-24
    Changes: Non-polymer description
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description