Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant Complexed with L-methionine

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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The role of amino acid residues in the active site of L-methionine gamma-lyase from Pseudomonas putida.

Fukumoto, M.Kudou, D.Murano, S.Shiba, T.Sato, D.Tamura, T.Harada, S.Inagaki, K.

(2012) Biosci Biotechnol Biochem 76: 1275-1284

  • DOI: https://doi.org/10.1271/bbb.110906
  • Primary Citation of Related Structures:  
    3VK2, 3VK3, 3VK4

  • PubMed Abstract: 

    Cys116, Lys240*, and Asp241* (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine γ-lyase of Pseudomonas putida (MGL_Pp) are highly conserved among heterologous MGLs. In a previous study, we found that substitution of Cys116 for His led to a drastic increase in activity toward L-cysteine and a decrease in that toward L-methionine. In this study, we examined some properties of the C116H mutant by kinetic analysis and 3D structural analysis. We assumed that substitution of Cys116 for His broke the original hydrogen-bond network and that this induced a significant effect of Tyr114 as a general acid catalyst, possibly due to the narrow space in the active site. The C116H mutant acquired a novel β-elimination activity and lead a drastic conformation change in the histidine residue at position 116 by binding the substrate, suggesting that this His residue affects the reaction specificity of C116H. Furthermore, we suggest that Lys240* is important for substrate recognition and structural stability and that Asp241* is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240*, and Asp241* contributes to substrate specificity that is, to L-methionine recognition at the active site in MGL_Pp.

  • Organizational Affiliation

    Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan. kinagaki@cc.okayama-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine gamma-lyase
A, B, C, D
398Pseudomonas putidaMutation(s): 1 
Gene Names: mdeA
Find proteins for P13254 (Pseudomonas putida)
Explore P13254 
Go to UniProtKB:  P13254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13254
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.172α = 90
b = 152.954β = 90
c = 80.579γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection