spacer

Overview for MACiE Entry M0306

Version history

General Information

EC Number: 1.3.7.6 (A member of the Oxidoreductases, Acting on the CH-CH group of donors, With an iron-sulfur protein as acceptor)

Enzyme Name: phycoerythrobilin synthase

Biological Species: Prochlorococcus phage P-SSM2 (Virus)

Catalytic Chain UniprotKB Accession Codes:

  • Q58MU6 - Phycoerythrobilin synthase

Representative PDB Code: 2vck - STRUCTURE OF PHYCOERYTHROBILIN SYNTHASE PEBS FROM THECYANOPHAGE P-SSM2 IN COMPLEX WITH THE BOUND SUBSTRATEBILIVERDIN IXA (Resolution = 1.8 Å).

Catalytic CATH Codes:

  • Unassigned Domain

Display structure information

Overall Reaction:

Image of proton

Image of reduced ferredoxin

Image of biliverdin IX alpha

right arrow

Image of oxidised ferredoxin

Image of (3Z)-phycoerythrobilin

4 proton
C00080
CHEBI:24636
2 reduced ferredoxin
C00138
CHEBI:17513
biliverdin IX alpha
C00500
CHEBI:57991
2 oxidised ferredoxin
C00139
CHEBI:17908
(3Z)-phycoerythrobilin
C05912
CHEBI:57438

View similar reactions


Stepwise Description of the Reaction

Step 1The pyrrole ring amide functionality of the fourth ring undergoes tautomerisation.
Step 2Simultaneously, reduced ferredoxin delivers one electron to the biliverdin ring while a solvent molecule donates a proton. This generates a neutral radical species.
Step 3The single electron oxidised ferredoxin donates a second electron in conjunction with Asp105A donating a proton to the C15 position of biliverdin.
Step 4Asp105A initiates tautomerisation in the intermediate.
Step 5Asp105A is deprotonated in a stereospecific manner, completing the initial tautomerisation.
Step 6The pyrrole ring now undergoes a spontaneous tautomerisation.
Step 7A second ferredoxin donates an electron to the first pyrrole ring, initiating deprotonation of Asp206.
Step 8Asp105 activates the radical intermediate towards tautomersiation.
Step 9Asp105A acts as a stereospecific general acid at the C2 position of the radical intermediate.
Step 10The final electron transfer occurs with concurrent deprotonation of a solvent molecule.
Step 11Reprotonation of the two catalytic aspartate residues regenerates the active site.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Asp 105 A Side Chain
Asp 206 A Side Chain

References

  1. Y. Hagiwara et al. (2009), J. Biol. Chem., 285, 1000-1007. Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA).
    Medline: 19887371
  2. A. W. Busch et al. (2011), Biochem. J., 433, 469-476. Radical mechanism of cyanophage phycoerythrobilin synthase (PebS).
    Medline: 21050180
  3. T. Dammeyer et al. (2008), J. Biol. Chem., 283, 27547-27554. Phycoerythrobilin synthase (PebS) of a marine virus. Crystal structures of the biliverdin complex and the substrate-free form.
    Medline: 18662988
  4. F. Y. Chiu et al. (2010), J. Biol. Chem., 285, 5056-5065. Electrostatic interaction of phytochromobilin synthase and ferredoxin for biosynthesis of phytochrome chromophore.
    Medline: 19996315

Homologue information for M0306 (2vck)

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

GOA logo
phytochromobilin biosynthetic process (biological process)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor (molecular function)
cobalt ion binding (molecular function)
oxidation-reduction process (biological process)
spacer
spacer