› 2dke

X-ray diffraction
2.5Å resolution

Crystal structure of substrate-free form of PcyA

Released:
DOI: 10.2210/pdb2dke/pdb
PDB entry 2dke coloured by chain, front view.
PDB entry 2dke coloured by chain, side view.
PDB entry 2dke coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803
Primary publication:
Induced-fitting and electrostatic potential change of PcyA upon substrate binding demonstrated by the crystal structure of the substrate-free form.
Hagiwara Y, Sugishima M, Takahashi Y, Fukuyama K
FEBS Lett 580 3823-8 (2006)
PMID: 16782089

Function and Biology Details

Reaction catalysed: 
(3Z)-phycocyanobilin + 4 oxidized ferredoxin = biliverdin IX-alpha + 4 reduced ferredoxin
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176303 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phycocyanobilin:ferredoxin oxidoreductase Chain: A
Molecule details ›
Chain: A
Length: 248 amino acids
Theoretical weight: 28.16 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Escherichia coli
UniProt:
  • Canonical: Q55891 (Residues: 1-248; Coverage: 100%)
Gene names: pcyA, slr0116
Sequence domains: Ferredoxin-dependent bilin reductase
Structure domains: oxygen-dependent coproporphyrinogen oxidase

Ligands and Environments

1 bound ligand:
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P43212
Unit cell:
a: 75.98Å b: 75.98Å c: 84.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.243 0.299
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Function and distribution of bilin biosynthesis enzymes in photosynthetic organisms.
Dammeyer et al. (2008)
11 other articles

1 mention without citation

Structural insights into proteasome activation by the 19S regulatory particle.
Ehlinger et al. (2013)