› 5x30

X-ray diffraction
1.7Å resolution

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.

Released:
DOI: 10.2210/pdb5x30/pdb
PDB entry 5x30 coloured by chain, front view.
PDB entry 5x30 coloured by chain, side view.
PDB entry 5x30 coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Structural and mechanistic insights into homocysteine degradation by a mutant of methionine γ-lyase based on substrate-assisted catalysis.
Sato D, Shiba T, Yunoto S, Furutani K, Fukumoto M, Kudou D, Tamura T, Inagaki K, Harada S
Protein Sci 26 1224-1230 (2017)
PMID: 28329912

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-146525 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
L-methionine gamma-lyase Chains: A, C
Molecule details ›
Chains: A, C
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
L-methionine gamma-lyase Chains: B, D
Molecule details ›
Chains: B, D
Length: 398 amino acids
Theoretical weight: 42.71 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

4 bound ligands:
Ligand HCS 2 x HCS
Ligand 4LM 1 x 4LM
Ligand H2S 1 x H2S
Ligand 7XF 1 x 7XF
1 modified residue:
Ligand LLP 2 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21212
Unit cell:
a: 153.753Å b: 152.971Å c: 80.586Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.195
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Structural Basis of the Inhibition of L-Methionine γ-Lyase from Fusobacterium nucleatum.
Bu et al. (2023)

2 mentions without citation

Effects of lifestyle interventions that include a physical activity component in class II and III obese individuals: a systematic review and meta-analysis.
Baillot et al. (2015)
1 more