4GW9

Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


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Literature

Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor.

Bellini, D.Papiz, M.Z.

(2012) Structure 20: 1436-1446

  • DOI: https://doi.org/10.1016/j.str.2012.06.002
  • Primary Citation of Related Structures:  
    4GW9

  • PubMed Abstract: 

    Phytochromes are photoreceptors in phototropic organisms that respond to light conditions by changing interactions between a response regulator and DNA. Bacterial phytochromes (BphPs) comprise an input photosensory core domain (PCD) and an output transducing domain (OTD). We report the structure of a BphP containing both PCD and the majority of its OTD, and demonstrate interaction with its cognate repressor. The OTD of RpBphP1, from Rhodopseudomonas palustris, is composed of a PAS/PAC domain and, to our knowledge, a hitherto unrecognized two-helix output sensor (HOS) domain. Unlike canonical BphPs, it does not transmit phosphorelay signals but forms a complex with the transcriptional repressor RpPpsR2 on photoconversion with far-red light. We show that HOS is essential for complex formation and that the anti-parallel dimer geometry is crucial in achieving HOS domain activation and protomer swapping under the control of light. These results provide insights into the steps taken by a two-component signaling system.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
bacteriophytochrome
A, B, C, D
655Rhodopseudomonas palustris CGA009Mutation(s): 0 
Gene Names: RPA1537
EC: 2.7.13.3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.94α = 90
b = 146.87β = 101.17
c = 139.55γ = 90
Software Package:
Software NamePurpose
GDAdata collection
SHARPphasing
REFMACrefinement
xia2data reduction
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary