2X9I

Structure of the Mutant D105N of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in complex with bound substrate Biliverdin IXA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Radical Mechanism of Cyanophage Phycoerythrobilin Synthase (Pebs).

Busch, A.W.U.Reijerse, E.J.Lubitz, W.Hofmann, E.Frankenberg-Dinkel, N.

(2011) Biochem.J. 433: 469

  • DOI: 10.1042/BJ20101642
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PEB (phycoerythrobilin) is a pink-coloured open-chain tetrapyrrole molecule found in the cyanobacterial light-harvesting phycobilisome. Within the phycobilisome, PEB is covalently bound via thioether bonds to conserved cysteine residues of the phycob ...

    PEB (phycoerythrobilin) is a pink-coloured open-chain tetrapyrrole molecule found in the cyanobacterial light-harvesting phycobilisome. Within the phycobilisome, PEB is covalently bound via thioether bonds to conserved cysteine residues of the phycobiliprotein subunits. In cyanobacteria, biosynthesis of PEB proceeds via two subsequent two-electron reductions catalysed by the FDBRs (ferredoxin-dependent bilin reductases) PebA and PebB starting from the open-chain tetrapyrrole biliverdin IXα. A new member of the FDBR family has been identified in the genome of a marine cyanophage. In contrast with the cyanobacterial enzymes, PebS (PEB synthase) from cyanophages combines both two-electron reductions for PEB synthesis. In the present study we show that PebS acts via a substrate radical mechanism and that two conserved aspartate residues at position 105 and 206 are critical for stereospecific substrate protonation and conversion. On the basis of the crystal structures of both PebS mutants and presented biochemical and biophysical data, a mechanism for biliverdin IXα conversion to PEB is postulated and discussed with respect to other FDBR family members.


    Organizational Affiliation

    Ruhr-University Bochum, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHYCOBILIN SYNTHASE
A, B, C, D
233Prochlorococcus phage P-SSM2Mutation(s): 1 
Gene Names: pebS
EC: 1.3.7.6
Find proteins for Q58MU6 (Prochlorococcus phage P-SSM2)
Go to UniProtKB:  Q58MU6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BLA
Query on BLA

Download SDF File 
Download CCD File 
A, B, C, D
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.920α = 109.38
b = 70.140β = 109.25
c = 81.970γ = 92.56
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-05-19
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance