6SAX

Chromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from Idiomarina species A28L (Pr-state monomer).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase.

Buhrke, D.Gourinchas, G.Muller, M.Michael, N.Hildebrandt, P.Winkler, A.

(2020) J.Biol.Chem. 295: 539-551

  • DOI: 10.1074/jbc.RA119.011915
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sensing of red and far-red light by bacteriophytochromes involves intricate interactions between their bilin chromophore and the protein environment. The light-triggered rearrangements of the cofactor configuration and eventually the protein conforma ...

    Sensing of red and far-red light by bacteriophytochromes involves intricate interactions between their bilin chromophore and the protein environment. The light-triggered rearrangements of the cofactor configuration and eventually the protein conformation enable bacteriophytochromes to interact with various protein effector domains for biological modulation of diverse physiological functions. Excitation of the holoproteins by red or far-red light promotes the photoconversion to their far red light-absorbing Pfr state or the red light-absorbing Pr state, respectively. Because prototypical bacteriophytochromes have a parallel dimer architecture, it is generally assumed that symmetric activation with two Pfr state protomers constitutes the signaling-active species. However, the bacteriophytochrome from Idiomarina species A28L (IsPadC) has recently been reported to enable long-range signal transduction also in asymmetric dimers containing only one Pfr protomer. By combining crystallography, hydrogen-deuterium exchange coupled to MS and vibrational spectroscopy, we show here that Pfr of IsPadC is in equilibrium with an intermediate "Pfr-like" state that combines features of Pfr and Meta-R states observed in other bacteriophytochromes. We also show that structural rearrangements in the N-terminal segment (NTS) can stabilize this Pfr-like state and that the PHY-tongue conformation of IsPadC is partially uncoupled from the initial changes in the NTS. This uncoupling enables structural asymmetry of the overall homodimeric assembly and allows signal transduction to the covalently linked physiological diguanylate cyclase output module in which asymmetry might play a role in the enzyme-catalyzed reaction. The functional differences to other phytochrome systems identified here highlight opportunities for using additional red-light sensors in artificial sensor-effector systems.


    Organizational Affiliation

    Technische Universit├Ąt Berlin, Germany.,Institute of Biochemistry, Graz University of Technology, Austria.,Max-Planck Institute for Medical Research, Germany.,Graz University of Technology, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diguanylate cyclase (GGDEF) domain-containing protein
B, A
314Idiomarina sp. A28LMutation(s): 0 
Find proteins for F7RW09 (Idiomarina sp. A28L)
Go to UniProtKB:  F7RW09
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LBV
Query on LBV

Download SDF File 
Download CCD File 
A, B
3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
2(R),3(E)- PHYTOCHROMOBILIN
C33 H37 N4 O6
DKMLMZVDTGOEGU-ISEYCTJISA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 149.960α = 90.00
b = 149.960β = 90.00
c = 77.520γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP32022

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references
  • Version 1.2: 2020-01-22
    Type: Database references