› 5b55

X-ray diffraction
2.14Å resolution

Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form

Released:
DOI: 10.2210/pdb5b55/pdb
PDB entry 5b55 coloured by chain, front view.
PDB entry 5b55 coloured by chain, side view.
PDB entry 5b55 coloured by chain, top view.
Source organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Primary publication:
Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen, Fusobacterium nucleatum.
Kezuka Y, Ishida T, Yoshida Y, Nonaka T
Biochem J 475 733-748 (2018)
PMID: 29343611

Function and Biology Details

Reaction catalysed: 
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185979 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tryptophan synthase beta chain-like PALP domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 340 amino acids
Theoretical weight: 38.56 KDa
Source organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8REP3 (Residues: 2-336; Coverage: 100%)
Gene name: FN1055
Sequence domains: Pyridoxal-phosphate dependent enzyme
Structure domains: Rossmann fold

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
2 bound ligands:
Ligand 0JO 2 x 0JO
Ligand PEG 2 x PEG
1 modified residue:
Ligand MLY 72 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2
Unit cell:
a: 191.046Å b: 57.127Å c: 94.293Å
α: 90° β: 100.89° γ: 90°
R-values:
R R work R free
0.203 0.201 0.237
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

Fusobacterium nucleatum Acts as a Pro-carcinogenic Bacterium in Colorectal Cancer: From Association to Causality.
Wang et al. (2021)
1 more