› 3vk4

X-ray diffraction
2.61Å resolution

Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine

Released:
DOI: 10.2210/pdb3vk4/pdb
PDB entry 3vk4 coloured by chain, front view.
PDB entry 3vk4 coloured by chain, side view.
PDB entry 3vk4 coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
The role of amino acid residues in the active site of L-methionine γ-lyase from Pseudomonas putida.
Fukumoto M, Kudou D, Murano S, Shiba T, Sato D, Tamura T, Harada S, Inagaki K
Biosci Biotechnol Biochem 76 1275-84 (2012)
PMID: 22785484

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146524 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-methionine gamma-lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 398 amino acids
Theoretical weight: 42.94 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
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand HCS 4 x HCS
1 modified residue:
Ligand LLP 4 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21212
Unit cell:
a: 153.488Å b: 153.487Å c: 80.671Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.191 0.253
Expression system: Escherichia coli

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Citations

1 review citation

Enzymes in Metabolic Anticancer Therapy.
Maggi et al. (2019)
12 other articles