5LLY

Photosensory Module of Bacteriophytochrome linked Diguanylyl Cyclase from Idiomarina species A28L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Long-range allosteric signaling in red light-regulated diguanylyl cyclases.

Gourinchas, G.Etzl, S.Gobl, C.Vide, U.Madl, T.Winkler, A.

(2017) Sci Adv 3: e1602498-e1602498

  • DOI: 10.1126/sciadv.1602498
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nature has evolved an astonishingly modular architecture of covalently linked protein domains with diverse functionalities to enable complex cellular networks that are critical for cell survival. The coupling of sensory modules with enzymatic effecto ...

    Nature has evolved an astonishingly modular architecture of covalently linked protein domains with diverse functionalities to enable complex cellular networks that are critical for cell survival. The coupling of sensory modules with enzymatic effectors allows direct allosteric regulation of cellular signaling molecules in response to diverse stimuli. We present molecular details of red light-sensing bacteriophytochromes linked to cyclic dimeric guanosine monophosphate-producing diguanylyl cyclases. Elucidation of the first crystal structure of a full-length phytochrome with its enzymatic effector, in combination with the characterization of light-induced changes in conformational dynamics, reveals how allosteric light regulation is fine-tuned by the architecture and composition of the coiled-coil sensor-effector linker and also the central helical spine. We anticipate that consideration of molecular principles of sensor-effector coupling, going beyond the length of the characteristic linker, and the appreciation of dynamically driven allostery will open up new directions for the design of novel red light-regulated optogenetic tools.


    Organizational Affiliation

    Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diguanylate cyclase (GGDEF) domain-containing protein
D, A, C, B
529Idiomarina sp. A28LMutation(s): 0 
Find proteins for F7RW09 (Idiomarina sp. A28L)
Go to UniProtKB:  F7RW09
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LBV
Query on LBV

Download SDF File 
Download CCD File 
A, B, C, D
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
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.500α = 90.00
b = 129.000β = 96.34
c = 122.010γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP27124

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Data collection
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence