› 1ycl

X-ray diffraction
1.8Å resolution

Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate

Released:
DOI: 10.2210/pdb1ycl/pdb
PDB entry 1ycl coloured by chain, front view.
PDB entry 1ycl coloured by chain, side view.
PDB entry 1ycl coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate.
Rajan R, Zhu J, Hu X, Pei D, Bell CE
Biochemistry 44 3745-53 (2005)
PMID: 15751951

Function and Biology Details

Reaction catalysed: 
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128577 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
S-ribosylhomocysteine lyase Chain: A
Molecule details ›
Chain: A
Length: 156 amino acids
Theoretical weight: 17.57 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O34667 (Residues: 2-157; Coverage: 99%)
Gene names: BSU30670, luxS, ytjB
Sequence domains: S-Ribosylhomocysteinase (LuxS)
Structure domains: S-ribosylhomocysteinase (LuxS)

Ligands and Environments

3 bound ligands:
Ligand CO 1 x CO
Ligand SO4 1 x SO4
Ligand KRI 1 x KRI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P6522
Unit cell:
a: 62.53Å b: 62.53Å c: 149.65Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.225 0.256
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

AI-2-mediated signalling in bacteria.
Pereira et al. (2013)
4 more

4 mentions without citation

Multi-scale computational enzymology: enhancing our understanding of enzymatic catalysis.
Gherib et al. (2013)
3 more