› 7f1u

X-ray diffraction
2.4Å resolution

Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-methionine intermediates

Released:
DOI: 10.2210/pdb7f1u/pdb
PDB entry 7f1u coloured by chain, front view.
PDB entry 7f1u coloured by chain, side view.
PDB entry 7f1u coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Characterization and application of l-methionine γ-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine.
Okawa A, Handa H, Yasuda E, Murota M, Kudo D, Tamura T, Shiba T, Inagaki K
J Biosci Bioeng 133 213-221 (2022)
PMID: 34953671

Function and Biology Details

Reactions catalysed: 
(1a) L-methionine = methanethiol + 2-aminobut-2-enoate
(1a) L-homocysteine = hydrogen sulfide + 2-aminobut-2-enoate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-537187 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
L-methionine gamma-lyase Chains: A, C, D
Molecule details ›
Chains: A, C, D
Length: 398 amino acids
Theoretical weight: 42.63 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli
UniProt:
  • Canonical: P13254 (Residues: 1-398; Coverage: 100%)
Gene name: mdeA
Sequence domains: Cys/Met metabolism PLP-dependent enzyme
L-methionine gamma-lyase Chain: B
Molecule details ›
Chain: B
Length: 398 amino acids
Theoretical weight: 42.86 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli
UniProt:
  • Canonical: P13254 (Residues: 1-398; Coverage: 100%)
Gene name: mdeA
Sequence domains: Cys/Met metabolism PLP-dependent enzyme

Ligands and Environments

2 bound ligands:
Ligand 3LM 3 x 3LM
Ligand MET 1 x MET
1 modified residue:
Ligand LLP 1 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21212
Unit cell:
a: 153.907Å b: 152.557Å c: 80.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.219
Expression system: Escherichia coli

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