2VEA

The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of a Complete Phytochrome Sensory Module in the Pr Ground State.

Essen, L.-O.Mailliet, J.Hughes, J.

(2008) Proc.Natl.Acad.Sci.USA 105: 14709

  • DOI: 10.1073/pnas.0806477105

  • PubMed Abstract: 
  • Phytochromes are red/far-red photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is s ...

    Phytochromes are red/far-red photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is still unclear. Here, we report the ground state structure of the complete sensory module of Cph1 phytochrome from the cyanobacterium Synechocystis 6803. Although the phycocyanobilin (PCB) chromophore is attached to Cys-259 as expected, paralleling the situation in plant phytochromes but contrasting to that in bacteriophytochromes, the ZZZssa conformation does not correspond to that expected from Raman spectroscopy. We show that the PHY domain, previously considered unique to phytochromes, is structurally a member of the GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) family. Indeed, the tandem-GAF dumbbell revealed for phytochrome sensory modules is remarkably similar to the regulatory domains of cyclic nucleotide (cNMP) phosphodiesterases and adenylyl cyclases. A unique feature of the phytochrome structure is a long, tongue-like protrusion from the PHY domain that seals the chromophore pocket and stabilizes the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. The structure that we present provides a framework for light-driven signal transmission in phytochromes.


    Organizational Affiliation

    Structural Biochemistry, Department of Chemistry, Philipps University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany. essen@chemie.uni-marburg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHYTOCHROME-LIKE PROTEIN CPH1
A
520Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: cph1
EC: 2.7.13.3
Find proteins for Q55168 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55168
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download SDF File 
Download CCD File 
A
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.180α = 90.00
b = 77.180β = 90.00
c = 249.000γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2014-02-26
    Type: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance