Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+:L-Hcy complex, Se-Met)

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase.

Evans, J.C.Huddler, D.P.Hilgers, M.T.Romanchuk, G.Matthews, R.G.Ludwig, M.L.

(2004) Proc Natl Acad Sci U S A 101: 3729-3736

  • DOI: https://doi.org/10.1073/pnas.0308082100
  • Primary Citation of Related Structures:  
    1Q7M, 1Q7Q, 1Q7Z, 1Q85, 1Q8A, 1Q8J

  • PubMed Abstract: 

    B(12)-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a different arrangement of modules. In the catalytic cycle, the cobalamin-binding domain carries methylcobalamin to the homocysteine (Hcy) domain to form methionine and returns cob(I)alamin to the folate (Fol) domain for remethylation by methyltetrahydrofolate (CH(3)-H(4)folate). Here, we describe crystal structures of a fragment of MetH from Thermotoga maritima comprising the domains that bind Hcy and CH(3)-H(4)folate. These substrate-binding domains are (beta alpha)(8) barrels packed tightly against one another with their barrel axes perpendicular. The properties of the domain interface suggest that the two barrels remain associated during catalysis. The Hcy and CH(3)-H(4)folate substrates are bound at the C termini of their respective barrels in orientations that position them for reaction with cobalamin, but the two active sites are separated by approximately 50 A. To complete the catalytic cycle, the cobalamin-binding domain must travel back and forth between these distant active sites.

  • Organizational Affiliation

    Department of Biological Chemistry and Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-methyltetrahydrofolate S-homocysteine methyltransferase
A, B
566Thermotoga maritimaMutation(s): 10 
Find proteins for Q9WYA5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYA5 
Go to UniProtKB:  Q9WYA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYA5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.12α = 90
b = 86.19β = 99.99
c = 126.08γ = 90
Software Package:
Software NamePurpose
MAR345data 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: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Structure summary