Crystal structure of Citrobacter freundii methionine gamma-lyase with V358Y replacement

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

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This is version 1.2 of the entry. See complete history


Engineering methionine gamma-lyase from Citrobacter freundii for anticancer activity.

Raboni, S.Revtovich, S.Demitri, N.Giabbai, B.Storici, P.Cocconcelli, C.Faggiano, S.Rosini, E.Pollegioni, L.Galati, S.Buschini, A.Morozova, E.Kulikova, V.Nikulin, A.Gabellieri, E.Cioni, P.Demidkina, T.Mozzarelli, A.

(2018) Biochim Biophys Acta Proteins Proteom 1866: 1260-1270

  • DOI: https://doi.org/10.1016/j.bbapap.2018.09.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Methionine deprivation of cancer cells, which are deficient in methionine biosynthesis, has been envisioned as a therapeutic strategy to reduce cancer cell viability. Methionine γ-lyase (MGL), an enzyme that degrades methionine, has been exploited to selectively remove the amino acid from cancer cell environment. In order to increase MGL catalytic activity, we performed sequence and structure conservation analysis of MGLs from various microorganisms. Whereas most of the residues in the active site and at the dimer interface were found to be conserved, residues located in the C-terminal flexible loop, forming a wall of the active site entry channel, were found to be variable. Therefore, we carried out site-saturation mutagenesis at four independent positions of the C-terminal flexible loop, P357, V358, P360 and A366 of MGL from Citrobacter freundii, generating libraries that were screened for activity. Among the active variants, V358Y exhibits a 1.9-fold increase in the catalytic rate and a 3-fold increase in K M , resulting in a catalytic efficiency similar to wild type MGL. V358Y cytotoxic activity was assessed towards a panel of cancer and nonmalignant cell lines and found to exhibit IC 50 lower than the wild type. The comparison of the 3D-structure of V358Y MGL with other MGL available structures indicates that the C-terminal loop is either in an open or closed conformation that does not depend on the amino acid at position 358. Nevertheless, mutations at this position allosterically affects catalysis.

  • Organizational Affiliation

    Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine gamma-lyase398Citrobacter freundiiMutation(s): 1 
Gene Names: AN672_11005BED45_02240BEH73_12300CfB38_0199HMPREF3212_02785TO64_18625
Find proteins for A0A0A5P8W7 (Citrobacter freundii)
Explore A0A0A5P8W7 
Go to UniProtKB:  A0A0A5P8W7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A5P8W7
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSO
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.667α = 90
b = 122.872β = 90
c = 127.515γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Council of Italy (CNR)ItalyMD P01.008
Russian Foundation for Basic ResearchRussian Federation15-54-78021

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description