9QM6 | pdb_00009qm6

Crystal structure of highly stable methionine gamma-lyase from Thermobrachium celere in complex with PLP and norleucine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.268 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

The methioninase from the alkalithermophile Thermobrachium celere possesses suitable properties for treatment of cancer.

Ferchaud, N.Kopecny, D.Perina, M.Boyer, A.Hentati, S.Pontoizeau, C.Desterke, C.Krystof, V.Machover, D.Briozzo, P.

(2025) Int J Biol Macromol 330: 147876-147876

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.147876
  • Primary Citation of Related Structures:  
    9QM6

  • PubMed Abstract: 

    L-Methionine deprivation for cancer treatment requires pyridoxal 5'-phosphate (PLP)-dependent L-methionine γ-lyases (MGL) with sustained activity in plasma. We investigated the MGL from the alkaliphilic thermophile Thermobrachium celere (TcMGL), which was compared to that from Pseudomonas putida (PpMGL) as a reference. Catalysis was limited to L-methionine, L-homocysteine, and L-cysteine, with highest catalytic efficiency towards L-methionine. Binding of apo-TcMGL to PLP results from an endothermic entropy-driven process, contrasting with apo-PpMGL that binds to cofactor following an exothermic enthalpy-driven reaction, as demonstrated with isothermal titration calorimetry. The tetrameric crystal structure of TcMGL revealed a mobile domain adopting open and closed conformations, regulating access of substrate and PLP to the active site. TcMGL exhibited great stability in human plasma in vitro. Half-life of the active enzyme increased from 9.2 h to 66.7 h with increasing PLP concentration, in much greater magnitude than that of PpMGL. Two-way ANOVA demonstrated a highly significant effect on half-lives of enzyme type and PLP concentration. The enzyme eliminated L-methionine from human plasma and exerted potent cytotoxicity against human carcinoma cells in vitro. TcMGL favourable characteristics make it a suitable candidate for treatment of cancer.


  • Organizational Affiliation
    • University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000, Versailles, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-methionine gamma-lyase
A, B, C, D
419Thermobrachium celereMutation(s): 0 
Gene Names: TCEL_00634
EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt
Find proteins for R7RTI8 (Thermobrachium celere DSM 8682)
Explore R7RTI8 
Go to UniProtKB:  R7RTI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR7RTI8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.268 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.426α = 90
b = 86.426β = 90
c = 862.41γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
Cootmodel building
PHASERphasing
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
autoPROCdata processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech Republic8J23FR011
Agence Nationale de la Recherche (ANR)Francethe Jean d'Alembert fellowship as part of France 2030 program ANR-11-IDEX-0003
Other privateIMEBATRACA
Other governmentFR 49271QH PHC BARRANDE

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release