› 4iyo

X-ray diffraction
1.8Å resolution

Crystal structure of cystathionine gamma lyase from Xanthomonas oryzae pv. oryzae (XometC) in complex with E-site serine, A-site serine, A-site external aldimine structure with aminoacrylate and A-site iminopropionate intermediates

Released:
DOI: 10.2210/pdb4iyo/pdb
PDB entry 4iyo coloured by chain, front view.
PDB entry 4iyo coloured by chain, side view.
PDB entry 4iyo coloured by chain, top view.
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Primary publication:
PLP undergoes conformational changes during the course of an enzymatic reaction.
Ngo HP, Cerqueira NM, Kim JK, Hong MK, Fernandes PA, Ramos MJ, Kang LW
Acta Crystallogr D Biol Crystallogr 70 596-606 (2014)
PMID: 24531493

Function and Biology Details

Reaction catalysed: 
(1a) L-cystathionine = L-cysteine + 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-177165 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cystathionine gamma-lyase-like protein Chain: A
Molecule details ›
Chain: A
Length: 397 amino acids
Theoretical weight: 42.64 KDa
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5H4T8 (Residues: 1-397; Coverage: 100%)
Gene names: XOO0778, metB
Sequence domains: Cys/Met metabolism PLP-dependent enzyme
Structure domains:
Cystathionine gamma-lyase-like protein Chains: B, C, D
Molecule details ›
Chains: B, C, D
Length: 397 amino acids
Theoretical weight: 42.86 KDa
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5H4T8 (Residues: 1-397; Coverage: 100%)
Gene names: XOO0778, metB
Sequence domains: Cys/Met metabolism PLP-dependent enzyme
Structure domains:

Ligands and Environments

6 bound ligands:
Ligand SER 5 x SER
Ligand GOL 3 x GOL
Ligand SO4 1 x SO4
Ligand 0JO 1 x 0JO
Ligand NAK 2 x NAK
Ligand PYR 1 x PYR
1 modified residue:
Ligand LLP 3 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P212121
Unit cell:
a: 76.319Å b: 86.344Å c: 226.344Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.138 0.136 0.18
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Current Advances on Structure-Function Relationships of Pyridoxal 5'-Phosphate-Dependent Enzymes.
Liang et al. (2019)
9 other articles

1 mention without citation

Catalytic specificity of the Lactobacillus plantarum cystathionine γ-lyase presumed by the crystallographic analysis.
Matoba et al. (2020)