Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with glycine

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.230 

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This is version 1.3 of the entry. See complete history


Crystal structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of alpha- and beta-protons of competitive inhibitors.

Revtovich, S.V.Faleev, N.G.Morozova, E.A.Anufrieva, N.V.Nikulin, A.D.Demidkina, T.V.

(2014) Biochimie 101: 161-167

  • DOI: https://doi.org/10.1016/j.biochi.2014.01.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional structure of the external aldimine of Citrobacter freundii methionine γ-lyase with competitive inhibitor glycine has been determined at 2.45 Å resolution. It revealed subtle conformational changes providing effective binding of the inhibitor and facilitating labilization of Cα-protons of the external aldimine. The structure shows that 1, 3-prototropic shift of Cα-proton to C4'-atom of the cofactor may proceed with participation of active site Lys210 residue whose location is favorable for performing this transformation by a concerted mechanism. The observed stereoselectivity of isotopic exchange of enantiotopic Cα-protons of glycine may be explained on the basis of external aldimine structure. The exchange of Cα-pro-(R)-proton of the external aldimine might proceed in the course of the concerted transfer of the proton from Cα-atom of glycine to C4'-atom of the cofactor. The exchange of Cα-pro-(S)-proton may be performed with participation of Tyr113 residue which should be present in its basic form. The isotopic exchange of β-protons, which is observed for amino acids bearing longer side groups, may be effected by two catalytic groups: Lys210 in its basic form, and Tyr113 acting as a general acid.

  • Organizational Affiliation

    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine gamma-lyase398Citrobacter freundiiMutation(s): 0 
Gene Names: megL
Find proteins for Q84AR1 (Citrobacter freundii)
Explore Q84AR1 
Go to UniProtKB:  Q84AR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84AR1
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.230 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.288α = 90
b = 123.052β = 90
c = 126.748γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection