› 3aep

X-ray diffraction
2.28Å resolution

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate

Released:
DOI: 10.2210/pdb3aep/pdb
PDB entry 3aep coloured by chain, front view.
PDB entry 3aep coloured by chain, side view.
PDB entry 3aep coloured by chain, top view.
Source organism: Entamoeba histolytica
Entry authors: Karaki T, Sato D, Shimizu A, Nozaki T, Harada S

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183128 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methionine gamma-lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 389 amino acids
Theoretical weight: 42.35 KDa
Source organism: Entamoeba histolytica
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86D28 (Residues: 1-389; Coverage: 100%)
Gene name: metg
Sequence domains: Cys/Met metabolism PLP-dependent enzyme
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand 4LM 4 x 4LM
Ligand MEE 2 x MEE
Ligand SO4 4 x SO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 99.215Å b: 85.359Å c: 114.649Å
α: 90° β: 101.99° γ: 90°
R-values:
R R work R free
0.158 0.156 0.198
Expression system: Escherichia coli

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