› 4iy7

X-ray diffraction
1.7Å resolution

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

Released:
DOI: 10.2210/pdb4iy7/pdb
PDB entry 4iy7 coloured by chain, front view.
PDB entry 4iy7 coloured by chain, side view.
PDB entry 4iy7 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:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177166 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cystathionine gamma-lyase-like protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
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:

Ligands and Environments

6 bound ligands:
Ligand SER 4 x SER
Ligand GOL 2 x GOL
Ligand SO4 1 x SO4
Ligand 0JO 1 x 0JO
Ligand PYR 2 x PYR
Ligand KOU 3 x KOU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P212121
Unit cell:
a: 76.219Å b: 86.069Å c: 225.997Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.136 0.134 0.169
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

2 mentions without citation

On Characterizing the Interactions between Proteins and Guanine Quadruplex Structures of Nucleic Acids.
McRae et al. (2017)
1 more