5LLY | pdb_00005lly

Photosensory Module of Bacteriophytochrome linked Diguanylyl Cyclase from Idiomarina species A28L

• PDB DOI: https://doi.org/10.2210/pdb5LLY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Idiomarina sp. A28L
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-28 Released: 2017-03-15 
• 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: 2.40 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

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

• PubMed: 28275738 
• DOI: https://doi.org/10.1126/sciadv.1602498
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria.
Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany.; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany.; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.; Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, 8010 Graz, Austria.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 243.35 kDa 
• Atom Count: 16,833 
• Modeled Residue Count: 2,013 
• Deposited Residue Count: 2,116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diguanylate cyclase (GGDEF) domain-containing protein	A [auth D], B [auth A], C, D [auth B]	529	Idiomarina sp. A28L	Mutation(s): 0  Gene Names: A28LD_0430
UniProt
Find proteins for A0ACD6B9P8 (Idiomarina sp. A28L) Explore A0ACD6B9P8  Go to UniProtKB:  A0ACD6B9P8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBV	E [auth D], H [auth A], L [auth C], P [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
GOL	K [auth A], O [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth D], G [auth D], I [auth A], J [auth A], M [auth C], N [auth C], Q [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.5	α = 90
b = 129	β = 96.34
c = 122.01	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-15 
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: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Data collection
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Structure summary