2X9J

Structure of the Mutant D206N of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in complex with bound substrate Biliverdin IXA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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This is version 1.3 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: https://doi.org/10.1042/BJ20101642
  • Primary Citation of Related Structures:  
    2X9I, 2X9J

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHYCOERYTHROBILIN SYNTHASE
A, B
233Prochlorococcus phage P-SSM2Mutation(s): 1 
EC: 1.3.7.6
UniProt
Find proteins for Q58MU6 (Prochlorococcus phage P-SSM2)
Explore Q58MU6 
Go to UniProtKB:  Q58MU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58MU6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.81α = 90
b = 63.15β = 108.53
c = 81.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-05-19
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description