Crystal Structure of the Photoactive Yellow Protein Domain from the Sensor Histidine Kinase Ppr from Rhodospirillum centenum

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal Structure of a Photoactive Yellow Protein from a Sensor Histidine Kinase: Conformational Variability and Signal Transduction

Rajagopal, S.Moffat, K.

(2003) Proc Natl Acad Sci U S A 100: 1649-1654

  • DOI: https://doi.org/10.1073/pnas.0336353100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Photoactive yellow protein (E-PYP) is a blue light photoreceptor, implicated in a negative phototactic response in Ectothiorhodospira halophila, that also serves as a model for the Per-Arnt-Sim superfamily of signaling molecules. Because no biological signaling partner for E-PYP has been identified, it has not been possible to correlate any of its photocycle intermediates with a relevant signaling state. However, the PYP domain (Ppr-PYP) from the sensor histidine kinase Ppr in Rhodospirillum centenum, which regulates the catalytic activity of Ppr by blue light absorption, may allow such issues to be addressed. Here we report the crystal structure of Ppr-PYP at 2 A resolution. This domain has the same absorption spectrum and similar photocycle kinetics as full length Ppr, but a blue-shifted absorbance and considerably slower photocycle than E-PYP. Although the overall fold of Ppr-PYP resembles that of E-PYP, a novel conformation of the beta 4-beta 5 loop results in inaccessibility of Met-100, thought to catalyze chromophore reisomerization, to the chromophore. This conformation also exposes a highly conserved molecular surface that could interact with downstream signaling partners. Other structural differences in the alpha 3-alpha 4 and beta 4-beta 5 loops are consistent with these regions playing significant roles in the control of photocycle dynamics and, by comparison to other sensory Per-Arnt-Sim domains, in signal transduction. Because of its direct linkage to a measurable biological output, Ppr-PYP serves as an excellent system for understanding how changes in photocycle dynamics affect signaling by PYPs.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
129Rhodospirillum centenumMutation(s): 0 
Gene Names: pph
Find proteins for Q9X2W8 (Rhodospirillum centenum)
Explore Q9X2W8 
Go to UniProtKB:  Q9X2W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X2W8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.56α = 90
b = 143.07β = 117.96
c = 36.45γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance