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PDBsum entry 1gc0

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protein Protein-protein interface(s) links
Lyase PDB id
1gc0
Jmol
Contents
Protein chains
355 a.a. *
Waters ×1258
* Residue conservation analysis
PDB id:
1gc0
Name: Lyase
Title: Crystal structure of the pyridoxal-5'-phosphate dependent l- methionine gamma-lyase from pseudomonas putida
Structure: Methionine gamma-lyase. Chain: a, b, c, d. Ec: 4.4.1.11
Source: Pseudomonas putida. Organism_taxid: 303
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.210     R-free:   0.236
Authors: H.Motoshima,K.Inagaki,T.Kumasaka,M.Furuichi,H.Inoue, T.Tamura,N.Esaki,K.Soda,N.Tanaka,M.Yamamoto,H.Tanaka
Key ref: H.Motoshima et al. (2000). Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida. J Biochem, 128, 349-354. PubMed id: 10965031
Date:
06-Jul-00     Release date:   08-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13254  (MEGL_PSEPU) -  Methionine gamma-lyase
Seq:
Struc:
398 a.a.
355 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.4.1.11  - Methionine gamma-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-methionine + H2O = methanethiol + NH3 + 2-oxobutanoate
L-methionine
+ H(2)O
= methanethiol
+ NH(3)
+ 2-oxobutanoate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
J Biochem 128:349-354 (2000)
PubMed id: 10965031  
 
 
Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida.
H.Motoshima, K.Inagaki, T.Kumasaka, M.Furuichi, H.Inoue, T.Tamura, N.Esaki, K.Soda, N.Tanaka, M.Yamamoto, H.Tanaka.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20146062 A.S.El-Sayed (2010).
Microbial L-methioninase: production, molecular characterization, and therapeutic applications.
  Appl Microbiol Biotechnol, 86, 445-467.  
18219122 A.Nikulin, S.Revtovich, E.Morozova, N.Nevskaya, S.Nikonov, M.Garber, and T.Demidkina (2008).
High-resolution structure of methionine gamma-lyase from Citrobacter freundii.
  Acta Crystallogr D Biol Crystallogr, 64, 211-218.
PDB code: 2rfv
  18678935 D.Sato, T.Karaki, A.Shimizu, K.Kamei, S.Harada, and T.Nozaki (2008).
Crystallization and preliminary X-ray analysis of L-methionine gamma-lyase 1 from Entamoeba histolytica.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 697-699.  
17169919 A.Goyer, E.Collakova, Y.Shachar-Hill, and A.D.Hanson (2007).
Functional characterization of a methionine gamma-lyase in Arabidopsis and its implication in an alternative to the reverse trans-sulfuration pathway.
  Plant Cell Physiol, 48, 232-242.  
17223627 V.Ali, and T.Nozaki (2007).
Current therapeutics, their problems, and sulfur-containing-amino-acid metabolism as a novel target against infections by "amitochondriate" protozoan parasites.
  Clin Microbiol Rev, 20, 164-187.  
  17012806 D.Sato, W.Yamagata, K.Kamei, T.Nozaki, and S.Harada (2006).
Expression, purification and crystallization of L-methionine gamma-lyase 2 from Entamoeba histolytica.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1034-1036.  
16615855 I.V.Manukhov, D.V.Mamaeva, E.A.Morozova, S.M.Rastorguev, N.G.Faleev, T.V.Demidkina, and G.B.Zavilgelsky (2006).
L-methionine gamma-lyase from Citrobacter freundii: cloning of the gene and kinetic parameters of the enzyme.
  Biochemistry (Mosc), 71, 361-369.  
16012835 T.Takakura, T.Ito, S.Yagi, Y.Notsu, T.Itakura, T.Nakamura, K.Inagaki, N.Esaki, R.M.Hoffman, and A.Takimoto (2006).
High-level expression and bulk crystallization of recombinant L-methionine gamma-lyase, an anticancer agent.
  Appl Microbiol Biotechnol, 70, 183-192.  
  16511092 D.V.Mamaeva, E.A.Morozova, A.D.Nikulin, S.V.Revtovich, S.V.Nikonov, M.B.Garber, and T.V.Demidkina (2005).
Structure of Citrobacter freundii L-methionine gamma-lyase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 546-549.
PDB code: 1y4i
15574935 F.Amarita, M.Yvon, M.Nardi, E.Chambellon, J.Delettre, and P.Bonnarme (2004).
Identification and functional analysis of the gene encoding methionine-gamma-lyase in Brevibacterium linens.
  Appl Environ Microbiol, 70, 7348-7354.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.