8F71 | pdb_00008f71

Crystal structure of the histidine kinase domain of bacteriophytochrome RpBphP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 
    0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: other
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This is version 1.2 of the entry. See complete history


Literature

Mode of autophosphorylation in bacteriophytochromes RpBphP2 and RpBphP3.

Kumarapperuma, I.Tom, I.P.Bandara, S.Montano, S.Yang, X.

(2023) Photochem Photobiol Sci 22: 1257-1266

  • DOI: https://doi.org/10.1007/s43630-023-00366-9
  • Primary Citation of Related Structures:  
    8F71

  • PubMed Abstract: 

    Phytochromes are red-light photoreceptors that regulate a wide range of physiological processes in plants, fungi and bacteria. Canonical bacteriophytochromes are photosensory histidine kinases that undergo light-dependent autophosphorylation, thereby regulating cellular responses to red light via two-component signaling pathways. However, the molecular mechanism of kinase activation remains elusive for bacteriophytochromes. In particular, the directionality of autophosphorylation is still an open question in these dimeric photoreceptor kinases. In this work, we perform histidine kinase assays on two tandem bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris. By examining the kinase activities of full-length bacteriophytochromes and two loss-of-function mutants under different light conditions, we demonstrate that RpBphP2 and RpBphP3 undergo light-dependent trans-phosphorylation between protomers in both homodimeric and heterodimeric forms. We have further determined the crystal structure of the histidine kinase domains of RpBphP2 at 3.19 Å resolution. Based on structural comparisons and homology modeling, we also present a model to account for the actions of trans-autophosphorylation in bacteriophytochromes.


  • Organizational Affiliation
    • Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine kinase
A, B
261Rhodopseudomonas palustris CGA009Mutation(s): 0 
Gene Names: phyB1RPA3015
EC: 2.7.13.3
UniProt
Find proteins for Q6N5G3 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6N5G3 
Go to UniProtKB:  Q6N5G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N5G3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.851α = 90
b = 84.851β = 90
c = 346.06γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data scaling
AutoSolphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY024363

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary