› 2d1e

X-ray diffraction
1.51Å resolution

Crystal structure of PcyA-biliverdin complex

Released:
DOI: 10.2210/pdb2d1e/pdb
PDB entry 2d1e coloured by chain, front view.
PDB entry 2d1e coloured by chain, side view.
PDB entry 2d1e coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803
Primary publication:
Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phycocyanobilin.
Hagiwara Y, Sugishima M, Takahashi Y, Fukuyama K
Proc Natl Acad Sci U S A 103 27-32 (2006)
PMID: 16380422

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

2 bound ligands:
Ligand NA 1 x NA
Ligand BLA 1 x BLA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21212
Unit cell:
a: 70.826Å b: 94.997Å c: 42.675Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.157 0.183
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Plant type ferredoxins and ferredoxin-dependent metabolism.
Hanke et al. (2013)
2 more

6 mentions without citation

Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phycocyanobilin.
Hagiwara et al. (2006)
5 more