The photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.

Nagano, S.Scheerer, P.Zubow, K.Michael, N.Inomata, K.Lamparter, T.Krau, N.

(2016) J Biol Chem 291: 20674-20691

  • DOI: https://doi.org/10.1074/jbc.M116.739136
  • Primary Citation of Related Structures:  
    5HSQ, 5I5L

  • PubMed Abstract: 

    Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion.

  • Organizational Affiliation

    the Institute of Medical Physics and Biophysics (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriophytochrome protein501Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: Atu1990
Find proteins for Q7CY45 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q7CY45 
Go to UniProtKB:  Q7CY45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CY45
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.019α = 90
b = 173.019β = 90
c = 78.823γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB498-B2
German Research FoundationGermanySFB1078-B6
Queen Mary University of LondonUnited KingdomPostgraduate Research Studentship
University of London, Central Research FundUnited KingdomAR/CRF/B

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-10-05
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.4: 2021-06-23
    Changes: Advisory, Derived calculations