Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 157.64 kDa 
• Atom Count: 10,522 
• Modelled Residue Count: 1,291 
• Deposited Residue Count: 1,370 
• Unique protein chains: 1

 6ET7

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

• PDB DOI:  https://doi.org/10.2210/pdb6ET7/pdb

• Classification: TRANSFERASE
• Organism(s): Idiomarina sp. A28L
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-10-25 Released: 2018-06-13 
• Deposition Author(s): Gourinchas, G., Winkler, A.
• Funding Organization(s): Austrian Science Fund

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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 

Literature

Asymmetric activation mechanism of a homodimeric red light regulated photoreceptor.

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

(2018) Elife 7

• PubMed: 29869984 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diguanylate cyclase (GGDEF) domain-containing protein	A, B	685	Idiomarina sp. A28L	Mutation(s): 2  Gene Names: A28LD_0430
UniProt
Find proteins for F7RW09 (Idiomarina sp. A28L) Explore F7RW09  Go to UniProtKB:  F7RW09

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBV	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	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 = 49.46	α = 90
b = 78.42	β = 90
c = 443.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Gourinchas, G., Winkler, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P27124

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release