1GC0

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

• PDB DOI: https://doi.org/10.2210/pdb1GC0/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Mutation(s): No 


• Deposited: 2000-07-06 Released: 2002-05-08 
• Deposition Author(s): Motoshima, H., Inagaki, K., Kumasaka, T., Furuichi, M., Inoue, H., Tamura, T., Esaki, N., Soda, K., Tanaka, N., Yamamoto, M., Tanaka, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

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 128: 349-354

• PubMed: 10965031 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a022760
• Primary Citation of Related Structures:  
  1GC0, 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) 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.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 171.61 kDa 
• Atom Count: 12,053 
• Modelled Residue Count: 1,431 
• Deposited Residue Count: 1,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHIONINE GAMMA-LYASE	A, B, C, D	398	Pseudomonas putida	Mutation(s): 0  EC: 4.4.1.11
UniProt
Find proteins for P13254 (Pseudomonas putida) Explore P13254  Go to UniProtKB:  P13254

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.861	α = 70.56
b = 81.03	β = 63.17
c = 81.282	γ = 63.38

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-08 
Deposition Author(s): Motoshima, H., Inagaki, K., Kumasaka, T., Furuichi, M., Inoue, H., Tamura, T., Esaki, N., Soda, K., Tanaka, N., Yamamoto, M., Tanaka, H.

Revision History  

• Version 1.0: 2002-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references