2O7C

Crystal structure of L-methionine-lyase from Pseudomonas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the antitumour enzyme L-methionine gamma-lyase from Pseudomonas putida at 1.8 A resolution

Kudou, D.Misaki, S.Yamashita, M.Tamura, T.Takakura, T.Yoshioka, T.Yagi, S.Hoffman, R.M.Takimoto, A.Esaki, N.Inagaki, K.

(2007) J.Biochem.(Tokyo) 141: 535-544

  • DOI: 10.1093/jb/mvm055

  • PubMed Abstract: 
  • l-Methionine gamma-lyase (EC 4.4.1.11, MGL_Pp) from Pseudomonas putida is a multifunctional enzyme, which belongs to the gamma-family of pyridoxal-5'-phosphate (PLP) dependent enzymes. In this report, we demonstrate that the three-dimensional structu ...

    l-Methionine gamma-lyase (EC 4.4.1.11, MGL_Pp) from Pseudomonas putida is a multifunctional enzyme, which belongs to the gamma-family of pyridoxal-5'-phosphate (PLP) dependent enzymes. In this report, we demonstrate that the three-dimensional structure of MGL_Pp has been completely solved by the molecular replacement method to an R-factor of 20.4% at 1.8 A resolution. Detailed information of the overall structure of MGL_Pp supplies a clear picture of the substrate- and PLP-binding pockets. Tyr59 and Arg61 of neighbouring subunits, which are strongly conserved in other gamma-family enzymes, contact the phosphate group of PLP. These residues are important as the main anchor within the active site. Lys240, Asp241 and Arg61 of one partner monomer and Tyr114 and Cys116 of the other partner monomer form a hydrogen-bond network in the MGL active site which is specific for MGLs. It is also suggested that electrostatic interactions at the subunit interface are involved in the stabilization of the structural conformation. The detailed structure will facilitate the development of MGL_Pp as an anticancer drug.


    Organizational Affiliation

    Department of Biofunctional Chemistry, Graduate School of Natural Science and Technology, Okayama University, Okayama-Shi, Okayama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine gamma-lyase
A, B, C, D
398Pseudomonas putidaMutation(s): 0 
Gene Names: mdeA
EC: 4.4.1.11
Find proteins for P13254 (Pseudomonas putida)
Go to UniProtKB:  P13254
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 133.129α = 90.00
b = 133.129β = 90.00
c = 215.243γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
X-PLORphasing
HKL-2000data scaling
HKL-2000data collection
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance