› 2d1r

X-ray diffraction
1.6Å resolution

Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP

Released:
DOI: 10.2210/pdb2d1r/pdb
PDB entry 2d1r coloured by chain, front view.
PDB entry 2d1r coloured by chain, side view.
PDB entry 2d1r coloured by chain, top view.
Source organism: Luciola cruciata
Primary publication:
Structural basis for the spectral difference in luciferase bioluminescence.
Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H
Nature 440 372-6 (2006)
PMID: 16541080

Function and Biology Details

Reaction catalysed: 
D-firefly luciferin + O(2) + ATP = firefly oxyluciferin + CO(2) + AMP + diphosphate + light
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146485 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Luciferin 4-monooxygenase Chain: A
Molecule details ›
Chain: A
Length: 548 amino acids
Theoretical weight: 60.13 KDa
Source organism: Luciola cruciata
Expression system: Escherichia coli
UniProt:
  • Canonical: P13129 (Residues: 1-548; Coverage: 100%)
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand AMP 1 x AMP
Ligand OLU 1 x OLU
1 modified residue:
Ligand CSO 2 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P212121
Unit cell:
a: 57.612Å b: 181.402Å c: 52.743Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.184 0.21
Expression system: Escherichia coli

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Citations

40 review citations

High-throughput screening assays for the identification of chemical probes.
Inglese et al. (2007)
39 more

14 mentions without citation

Conformational dynamics in the Acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase.
Gulick AM. (2009)
13 more