6ET7

Activated heterodimer of the bacteriophytochrome regulated diguanylyl cyclase variant - S505V A526V - from Idiomarina species A28L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Asymmetric activation mechanism of a homodimeric red light regulated photoreceptor.

Gourinchas, G.Heintz, U.Winkler, A.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.34815
  • Primary Citation of Related Structures:  
    6ET7

  • PubMed Abstract: 

    Organisms adapt to environmental cues using diverse signaling networks. In order to sense and integrate light for regulating various biological functions, photoreceptor proteins have evolved in a modular way. This modularity is targeted in the development of optogenetic tools enabling the control of cellular events with high spatiotemporal precision. However, the limited understanding of signaling mechanisms impedes the rational design of innovative photoreceptor-effector couples. Here, we reveal molecular details of signal transduction in phytochrome-regulated diguanylyl cyclases. Asymmetric structural changes of the full-length homodimer result in a functional heterodimer featuring two different photoactivation states. Structural changes around the cofactors result in a quasi-translational rearrangement of the distant coiled-coil sensor-effector linker. Eventually, this regulates enzymatic activity by modulating the dimer interface of the output domains. Considering the importance of phytochrome heterodimerization in plant signaling, our mechanistic details of asymmetric photoactivation in a bacterial system reveal novel aspects of the evolutionary adaptation of phytochromes.


  • Organizational Affiliation

    Institute of Biochemistry, Graz University of Technology, Graz, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diguanylate cyclase (GGDEF) domain-containing protein
A, B
685Idiomarina sp. A28LMutation(s): 2 
Gene Names: A28LD_0430
EC: 2.7.7.65
UniProt
Find proteins for F7RW09 (Idiomarina sp. A28L)
Explore F7RW09 
Go to UniProtKB:  F7RW09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7RW09
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBV
Query on LBV

Download Ideal Coordinates CCD File 
C [auth A],
E [auth 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
C33 H37 N4 O6
DKMLMZVDTGOEGU-ISEYCTJISA-O
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.46α = 90
b = 78.42β = 90
c = 443.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP27124

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.2: 2024-10-09
    Changes: Structure summary