Neurospora crassa cobalamin-independent methionine synthase complexed with Zn2+

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Fungal cobalamin-independent methionine synthase: Insights from the model organism, Neurospora crassa.

Wheatley, R.W.Ng, K.K.Kapoor, M.

(2015) Arch Biochem Biophys 590: 125-137

  • DOI: https://doi.org/10.1016/j.abb.2015.11.037
  • Primary Citation of Related Structures:  
    4ZTX, 4ZTY

  • PubMed Abstract: 

    Two families of methionine synthases, distinct in catalytic and structural features, have been encountered: MetH, the cobalamin-dependent enzyme and MetE, the cobalamin-independent form. The MetE family is of mechanistic interest due to the chemically challenging nature of the reaction and is a potential target for antifungal therapeutics since the human genome encodes only MetH. Here we report the identification, purification, and crystal structure of MetE from the filamentous fungus Neurospora crassa (ncMetE). ncMetE was highly thermostable and crystallized readily, making it ideal for study. Crystal structures of native ncMetE in complex with either Zn(2+)or Cd(2+) were solved at resolution limits of 2.10 Å and 1.88 Å, respectively. The monomeric protein contains two domains, each containing a (βα)8 barrel core, and a long α-helical segment spans the length of the protein, connecting the domains. Zn(2+) bound in the C-terminal domain exhibits tetrahedral coordination with the side chains of His 652, Cys 654, Glu 676 and Cys 737. A Cd(2+) replete structure revealed a supermetalated enzyme and demonstrated the inate flexibility of the metal binding site. An extensive analysis of sequence conservation within the MetE family identified 57 highly conserved residues and 60 additional residues that were conserved in all fungal sequences examined.

  • Organizational Affiliation

    Division of Biochemistry, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, T2N 1N4, Canada. Electronic address: rob@wheatley.ca.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cobalamin-Independent Methionine synthase769Neurospora crassaMutation(s): 0 
Gene Names: met-8GE21DRAFT_4142
Find proteins for Q8X1E4 (Neurospora crassa)
Explore Q8X1E4 
Go to UniProtKB:  Q8X1E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X1E4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.254α = 90
b = 94.63β = 90
c = 114.907γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-30
    Changes: Database references
  • Version 1.2: 2016-01-06
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence