4E04

RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.

Bellini, D.Papiz, M.Z.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1058-1066

  • DOI: 10.1107/S0907444912020537
  • Primary Citation of Related Structures:  
    4E04

  • PubMed Abstract: 
  • Bacteriophytochromes (BphPs) are biliverdin IXα-containing photoreceptors that photoconvert between red (Pr) and far-red (Pfr) absorbing states. BphPs are one half of a two-component system that transmits a light signal to a histidine kinase domain and then to a gene-response regulator ...

    Bacteriophytochromes (BphPs) are biliverdin IXα-containing photoreceptors that photoconvert between red (Pr) and far-red (Pfr) absorbing states. BphPs are one half of a two-component system that transmits a light signal to a histidine kinase domain and then to a gene-response regulator. In Rhodopseudomonas palustris, synthesis of a light-harvesting complex (LH4) is controlled by two BphPs (RpBphP2 and RpBphP3). Despite their high sequence identity (52%), their absorption spectra are very different. The spectra of RpBphP2 exhibit classic Pr-to-Pfr photoconversion, whereas RpBphP3 quenches and a high-energy Pnr state emerges [Giraud et al. (2005), J. Biol. Chem. 280, 32389-32397]. Crystallization of the chromophore-binding domain (CBD) of RpBphP2 (RpBphP2-CBD) proved to be difficult and the structure of RpBphP3-CBD was used to crystallize RpBphP2-CBD* using homologue-directed mutagenesis. The structure shows that dimerization is an important factor in successful crystallization of RpBphP2-CBD* and arises from an N136R mutation. Mutations at this site correlate with an ability to dimerize in other truncated BphPs and may also be important for full-length dimer formation. Comparison of the RpBphP3-CBD and RpBphP2-CBD* biliverdin IXα pockets revealed that the former has additional hydrogen bonding around the B and D pyrrole rings that may constrain photoconversion to Pfr, resulting in a strained photoexcited Pnr state.


    Organizational Affiliation

    Institute of Integrative Biology, Liverpool University, Biosciences Building, Crown Street, Liverpool L69 7ZB, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1A, B327Rhodopseudomonas palustris CGA009Mutation(s): 15 
Gene Names: phyB1phyB2RPA3015RPA3016
EC: 2.7.13.3
Find proteins for Q6N5G3 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6N5G3 
Go to UniProtKB:  Q6N5G3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LBV
Query on LBV

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid
C33 H37 N4 O6
DKMLMZVDTGOEGU-ISEYCTJISA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.35α = 90
b = 79.86β = 90
c = 149.88γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Database references
  • Version 1.2: 2013-01-23
    Changes: Database references