5I5L

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1074/jbc.M116.739136
  • Primary Citation of Related Structures:  

  • 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 provid ...

    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

    From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriophytochrome protein
A
501Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Find proteins for Q7CY45 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  Q7CY45
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TAM
Query on TAM

Download SDF File 
Download CCD File 
A
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
BLA
Query on BLA

Download SDF File 
Download CCD File 
A
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 173.019α = 90.00
b = 173.019β = 90.00
c = 78.823γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-10-05
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence