Phycoerythrobilin synthase

 

Plays a role in phycoerythrobilin biosynthesis, the red pigment chromophore photosynthetically active biliproteins of a cyanophage infecting oceanic cyanobacteria of the Prochlorococcus genus. It uses a four electron reduction to carry out the reactions catalyses by EC 1.3.7.2 (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and EC 1.3.7.3 (phycoerythrobilin:ferredoxin oxidoreductase). 15,16-Dihydrobiliverdin is formed as a bound intermediate. Free 15,16-dihydrobiliverdin can also act as a substrate to form phycoerythrobilin.

 

Reference Protein and Structure

Sequence
Q58MU6 UniProt (1.3.7.6) IPR009249 (Sequence Homologues) (PDB Homologues)
Biological species
Prochlorococcus phage P-SSM2 (Virus) Uniprot
PDB
2vck - Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in Complex with the bound Substrate Biliverdin IXa (1.8 Å) PDBe PDBsum 2vck
Catalytic CATH Domains
3.40.1500.20 CATHdb (see all for 2vck)
Click To Show Structure

Enzyme Reaction (EC:1.3.7.6)

biliverdin(2-)
CHEBI:57991ChEBI
+
hydron
CHEBI:15378ChEBI
+
tetra-mu3-sulfido-tetrairon(1+)
CHEBI:33723ChEBI
→
(3Z)-phycoerythrobilin(2-)
CHEBI:57438ChEBI
+
tetra-mu3-sulfido-tetrairon(2+)
CHEBI:33722ChEBI
Alternative enzyme names: PebS,

Enzyme Mechanism

Introduction

Spectroscopic studies have shown the ring to adopt a number of protonation states throughout the reaction [PMID:21050180]. The pyrrole ring amide functionality of the fourth ring undergoes tautomerisation. Simultaneously, reduced ferredoxin delivers one electron to the biliverdin ring while a solvent molecule donates a proton. This generates a neutral radical species. The single electron oxidised ferredoxin donates a second electron in conjunction with Asp105A donating a proton to the C15 position of biliverdin. Asp105A initiates tautomerisation in the intermediate. Asp105A is deprotonated in a stereospecific manner, completing the initial tautomerisation. The pyrrole ring now undergoes a spontaneous tautomerisation. A second ferredoxin donates an electron to the first pyrrole ring, initiating deprotonation of Asp206. Asp105 activates the radical intermediate towards tautomersiation. Asp105A acts as a stereospecific general acid at the C2 position of the radical intermediate. The final electron transfer occurs with concurrent deprotonation of a solvent molecule. Reprotonation of the two catalytic aspartate residues regenerates the active site.

Catalytic Residues Roles

UniProt PDB* (2vck)
Asp206, Asp105 Asp206A, Asp105A Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

tautomerisation (not keto-enol), intermediate formation, overall reactant used, electron transfer, proton transfer, overall product formed, assisted tautomerisation (not keto-enol), assisted keto-enol tautomerisation, native state of enzyme regenerated, inferred reaction step

References

  1. Busch AW et al. (2011), Biochem J, 433, 469-476. Radical mechanism of cyanophage phycoerythrobilin synthase (PebS). DOI:10.1042/bj20101642. PMID:21050180.
  2. Hagiwara Y et al. (2010), J Biol Chem, 285, 1000-1007. Structural Insights into Vinyl Reduction Regiospecificity of Phycocyanobilin:Ferredoxin Oxidoreductase (PcyA). DOI:10.1074/jbc.m109.055632. PMID:19887371.
  3. Chiu FY et al. (2010), J Biol Chem, 285, 5056-5065. Electrostatic Interaction of Phytochromobilin Synthase and Ferredoxin for Biosynthesis of Phytochrome Chromophore. DOI:10.1074/jbc.m109.075747. PMID:19996315.
  4. Dammeyer T 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. DOI:10.1074/jbc.m803765200. PMID:18662988.

Step 1. The pyrrole ring amide functionality of the fourth ring undergoes tautomerisation.

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Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond donor
Asp206A hydrogen bond donor

Chemical Components

tautomerisation (not keto-enol), intermediate formation, overall reactant used

Step 2. Simultaneously, reduced ferredoxin delivers one electron to the biliverdin ring while a solvent molecule donates a proton. This generates a neutral radical species. The presence of a conserved region of positively charged residues on the protein surface binds the electron transfer protein ferredoxin. The ionisable carboxylate side chains on the biliverdin substrate are proposed to be involved in mediating electron transfer between the ferredoxin binding site and the internal lactam rings [PMID:19996315].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp206A hydrogen bond donor
Asp105A hydrogen bond donor

Chemical Components

electron transfer, proton transfer, intermediate formation, overall reactant used

Step 3. The single electron oxidised ferredoxin donates a second electron in conjunction with Asp105A donating a proton to the C15 position of biliverdin.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond donor
Asp206A hydrogen bond donor
Asp105A proton donor

Chemical Components

electron transfer, proton transfer, intermediate formation, overall product formed

Step 4. Asp105A initiates tautomerisation in the intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp206A hydrogen bond donor
Asp105A hydrogen bond acceptor
Asp105A proton acceptor

Chemical Components

assisted tautomerisation (not keto-enol), proton transfer, intermediate formation

Step 5. Asp105A is deprotonated in a stereospecific manner, completing the initial tautomerisation. The catalytic aspartate residues are positioned as to act as stereospecific general bases towards the reaction intermediates [PMID:19887371, PMID:21050180].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond donor, steric role
Asp206A hydrogen bond donor
Asp105A proton donor

Chemical Components

proton transfer, intermediate formation

Step 6. The pyrrole ring now undergoes a spontaneous tautomerisation.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond acceptor
Asp206A hydrogen bond donor

Chemical Components

tautomerisation (not keto-enol), intermediate formation

Step 7. A second ferredoxin donates an electron to the first pyrrole ring, initiating deprotonation of Asp206.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp206A hydrogen bond donor
Asp105A hydrogen bond acceptor
Asp206A proton donor

Chemical Components

electron transfer, proton transfer, overall reactant used, intermediate formation

Step 8. Asp105 activates the radical intermediate towards tautomersiation.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond acceptor
Asp206A hydrogen bond acceptor
Asp105A proton acceptor

Chemical Components

proton transfer, assisted keto-enol tautomerisation, intermediate formation

Step 9. Asp105A acts as a stereospecific general acid at the C2 position of the radical intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond donor, steric role
Asp206A hydrogen bond acceptor
Asp105A proton donor

Chemical Components

proton transfer

Step 10. The final electron transfer occurs with concurrent deprotonation of a solvent molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond acceptor
Asp206A hydrogen bond acceptor

Chemical Components

proton transfer, electron transfer, overall product formed, overall reactant used

Step 11. Reprotonation of the two catalytic aspartate residues regenerates the active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp105A hydrogen bond acceptor
Asp206A hydrogen bond acceptor, proton acceptor
Asp105A proton acceptor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. The pyrrole ring amide functionality of the fourth ring undergoes tautomerisation.

Step 2. Simultaneously, reduced ferredoxin delivers one electron to the biliverdin ring while a solvent molecule donates a proton. This generates a neutral radical species. The presence of a conserved region of positively charged residues on the protein surface binds the electron transfer protein ferredoxin. The ionisable carboxylate side chains on the biliverdin substrate are proposed to be involved in mediating electron transfer between the ferredoxin binding site and the internal lactam rings [PMID:19996315].

Step 3. The single electron oxidised ferredoxin donates a second electron in conjunction with Asp105A donating a proton to the C15 position of biliverdin.

Step 4. Asp105A initiates tautomerisation in the intermediate.

Step 5. Asp105A is deprotonated in a stereospecific manner, completing the initial tautomerisation. The catalytic aspartate residues are positioned as to act as stereospecific general bases towards the reaction intermediates [PMID:19887371, PMID:21050180].

Step 6. The pyrrole ring now undergoes a spontaneous tautomerisation.

Step 7. A second ferredoxin donates an electron to the first pyrrole ring, initiating deprotonation of Asp206.

Step 8. Asp105 activates the radical intermediate towards tautomersiation.

Step 9. Asp105A acts as a stereospecific general acid at the C2 position of the radical intermediate.

Step 10. The final electron transfer occurs with concurrent deprotonation of a solvent molecule.

Step 11. Reprotonation of the two catalytic aspartate residues regenerates the active site.

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday