5LLX

Bacteriophytochrome activated diguanylyl cyclase from Idiomarina species A28L with GTP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1126/sciadv.1602498
  • Primary Citation of Related Structures:  
    5LLW, 5LLX, 5LLY

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diguanylate cyclase (GGDEF) domain-containing protein
A, B
685Idiomarina sp. A28LMutation(s): 0 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBV
Query on LBV

Download Ideal Coordinates CCD File 
C [auth A],
G [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
GTP
Query on GTP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.73α = 90
b = 78.64β = 90
c = 452.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

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: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-10-23
    Changes: Structure summary