Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Metal active site elasticity linked to activation of homocysteine in methionine synthases.

Koutmos, M.Pejchal, R.Bomer, T.M.Matthews, R.G.Smith, J.L.Ludwig, M.L.

(2008) Proc Natl Acad Sci U S A 105: 3286-3291

  • DOI: https://doi.org/10.1073/pnas.0709960105
  • Primary Citation of Related Structures:  
    3BOF, 3BOL, 3BQ5, 3BQ6

  • PubMed Abstract: 

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  • Organizational Affiliation

    Biophysics Research Division, Life Sciences Institute, and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. mkoutmos@umich.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
A, B
766Thermotoga maritimaMutation(s): 0 
Gene Names: metE
Find proteins for Q9X112 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X112 
Go to UniProtKB:  Q9X112
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X112
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.229α = 90
b = 107.164β = 108.96
c = 107.667γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection