1GC0

CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida

Motoshima, H.Inagaki, K.Kumasaka, T.Furuichi, M.Inoue, H.Tamura, T.Esaki, N.Soda, K.Tanaka, N.Yamamoto, M.Tanaka, H.

(2000) J.BIOCHEM.(TOKYO) 128: 349-354

  • Primary Citation of Related Structures:  1GC2

  • PubMed Abstract: 
  • L-Methionine gamma-lyase (MGL) catalyzes the pyridoxal 5'-phosphate (PLP) dependent alpha,gamma-elimination of L-methionine. We have determined two crystal structures of MGL from Pseudomonas putida using MAD (multiwavelength anomalous diffraction) an ...

    L-Methionine gamma-lyase (MGL) catalyzes the pyridoxal 5'-phosphate (PLP) dependent alpha,gamma-elimination of L-methionine. We have determined two crystal structures of MGL from Pseudomonas putida using MAD (multiwavelength anomalous diffraction) and molecular replacement methods. The structures have been refined to an R-factor of 21.1% at 2.0 and 1.7 A resolution using synchrotron radiation diffraction data. A homotetramer with 222 symmetry is built up by non-crystallographic symmetry. Two monomers associate to build the active dimer. The spatial fold of subunits, with three functionally distinct domains and their quarternary arrangement, is similar to those of L-cystathionine beta-lyase and L-cystathionine gamma-synthase from Escherichia coli.


    Related Citations: 
    • Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution.
      Clausen, T.,Huber, R.,Prade, L.,Wahl, M.C.,Messerschmidt, A.
      (1998) Embo J. 17: 6827
    • Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
      Clausen, T.,Huber, R.,Laber, B.,Pohlenz, H.D.,Messerschmidt, A.
      (1996) J.Mol.Biol. 262: 202
    • Structural analysis of the L-methionine gamma-lyase gene from Pseudomonas putida.
      Inoue, H.,Inagaki, K.,Sugimoto, M.,Esaki, N.,Soda, K.,Tanaka, H.
      (1995) J.BIOCHEM.(TOKYO) 117: 1120


    Organizational Affiliation

    RIKEN Harima Institute, Kouto, Mikazuki, Sayo-gun, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHIONINE GAMMA-LYASE
A, B, C, D
398Pseudomonas putidaGene Names: mdeA
EC: 4.4.1.11
Find proteins for P13254 (Pseudomonas putida)
Go to UniProtKB:  P13254
Small Molecules
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: 0.236 
  • R-Value Work: 0.210 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 72.861α = 70.56
b = 81.030β = 63.17
c = 81.282γ = 63.38
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance