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PDBsum entry 3jw9

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protein ligands links
Lyase PDB id
3jw9

 

 

 

 

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Contents
Protein chain
396 a.a. *
Ligands
ECX
PEG
Waters ×330
* Residue conservation analysis
PDB id:
3jw9
Name: Lyase
Title: Crystal structure of l-methionine gamma-lyase from citrobacter freundii with s-ethyl-cysteine
Structure: Methionine gamma-lyase. Chain: a. Engineered: yes
Source: Citrobacter freundii. Organism_taxid: 546. Gene: megl. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.168     R-free:   0.199
Authors: S.V.Revtovish,A.D.Nikulin,E.A.Morozova,T.V.Demidkina
Key ref: S.V.Revtovich et al. (2011). Three-dimensional structures of noncovalent complexes of Citrobacter freundii methionine γ-lyase with substrates. Biochemistry (mosc), 76, 564-570. PubMed id: 21639836
Date:
18-Sep-09     Release date:   08-Sep-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q84AR1  (Q84AR1_CITFR) -  L-methionine gamma-lyase from Citrobacter freundii
Seq:
Struc:
398 a.a.
396 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.4.1.11  - methionine gamma-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-methionine + H2O = methanethiol + 2-oxobutanoate + NH4+
L-methionine
+ H2O
Bound ligand (Het Group name = ECX)
matches with 50.00% similarity
= methanethiol
+ 2-oxobutanoate
+ NH4(+)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Biochemistry (mosc) 76:564-570 (2011)
PubMed id: 21639836  
 
 
Three-dimensional structures of noncovalent complexes of Citrobacter freundii methionine γ-lyase with substrates.
S.V.Revtovich, E.A.Morozova, E.N.Khurs, L.N.Zakomirdina, A.D.Nikulin, T.V.Demidkina, R.M.Khomutov.
 
  ABSTRACT  
 
Crystal structures of Citrobacter freundii methionine γ-lyase complexes with the substrates of γ- (L-1-amino-3-methylthiopropylphosphinic acid) and β- (S-ethyl-L-cysteine) elimination reactions and the competitive inhibitor L-norleucine have been determined at 1.45, 1.8, and 1.63 Å resolution, respectively. All three amino acids occupy the active site of the enzyme but do not form a covalent bond with pyridoxal 5'-phosphate. Hydrophobic interactions between the active site residues and the side groups of the substrates and the inhibitor are supposed to cause noncovalent binding. Arg374 and Ser339 are involved in the binding of carboxyl groups of the substrates and the inhibitor. The hydroxyl of Tyr113 is a potential acceptor of a proton from the amino groups of the amino acids.
 

 

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