› 2vck

X-ray diffraction
1.8Å resolution

Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in Complex with the bound Substrate Biliverdin IXa

Released:
DOI: 10.2210/pdb2vck/pdb
PDB entry 2vck coloured by chain, front view.
PDB entry 2vck coloured by chain, side view.
PDB entry 2vck coloured by chain, top view.
Source organism: Prochlorococcus phage P-SSM2
Primary publication:
Phycoerythrobilin synthase (PebS) of a marine virus. Crystal structures of the biliverdin complex and the substrate-free form.
Dammeyer T, Hofmann E, Frankenberg-Dinkel N
J Biol Chem 283 27547-27554 (2008)
PMID: 18662988

Function and Biology Details

Reaction catalysed: 
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin = biliverdin IX-alpha + 2 reduced ferredoxin
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176753 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phycoerythrobilin synthase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 233 amino acids
Theoretical weight: 27.62 KDa
Source organism: Prochlorococcus phage P-SSM2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q58MU6 (Residues: 1-233; Coverage: 100%)
Gene names: PSSM2_058, pebS
Sequence domains: Ferredoxin-dependent bilin reductase
Structure domains: oxygen-dependent coproporphyrinogen oxidase

Ligands and Environments

1 bound ligand:
Ligand BLA 4 x BLA
1 modified residue:
Ligand MSE 28 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P1
Unit cell:
a: 53.56Å b: 67.57Å c: 81.28Å
α: 92.26° β: 109.07° γ: 106.58°
R-values:
R R work R free
0.187 0.184 0.225
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

Bacterial phytochromes: more than meets the light.
Auldridge et al. (2011)
3 more

2 mentions without citation

Ferredoxin-dependent bilin reductases in eukaryotic algae: Ubiquity and diversity.
Rockwell et al. (2017)
1 more