1W25

Response regulator PleD in complex with c-diGMP

• PDB DOI:  https://doi.org/10.2210/pdb1W25/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-06-28 Released: 2004-11-18 
• Deposition Author(s): Chan, C., Schirmer, T., Jenal, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Structural Basis of Activity and Allosteric Control of Diguanylate Cyclase

Chan, C., Paul, R., Samoray, D., Amiot, N., Giese, B., Jenal, U., Schirmer, T.

(2004) Proc Natl Acad Sci U S A 101: 17084

• PubMed: 15569936 
• DOI: https://doi.org/10.1073/pnas.0406134101
• Primary Citation of Related Structures:  
  1W25


• PubMed Abstract: 
  

Recent discoveries suggest that a novel second messenger, bis-(3'-->5')-cyclic di-GMP (c-diGMP), is extensively used by bacteria to control multicellular behavior. Condensation of two GTP to the dinucleotide is catalyzed by the widely distributed diguanylate cyclase (DGC or GGDEF) domain that occurs in various combinations with sensory and/or regulatory modules. The crystal structure of the unorthodox response regulator PleD from Caulobacter crescentus, which consists of two CheY-like receiver domains and a DGC domain, has been solved in complex with the product c-diGMP. PleD forms a dimer with the CheY-like domains (the stem) mediating weak monomer-monomer interactions. The fold of the DGC domain is similar to adenylate cyclase, but the nucleotide-binding mode is substantially different. The guanine base is H-bonded to Asn-335 and Asp-344, whereas the ribosyl and alpha-phosphate moieties extend over the beta2-beta3-hairpin that carries the GGEEF signature motif. In the crystal, c-diGMP molecules are crosslinking active sites of adjacent dimers. It is inferred that, in solution, the two DGC domains of a dimer align in a two-fold symmetric way to catalyze c-diGMP synthesis. Two mutually intercalated c-diGMP molecules are found tightly bound at the stem-DGC interface. This allosteric site explains the observed noncompetitive product inhibition. We propose that product inhibition is due to domain immobilization and sets an upper limit for the concentration of this second messenger in the cell.

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Organizational Affiliation: 

Divisions of Structural Biology and Molecular Microbiology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.

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)

Macromolecule Content

• Total Structure Weight: 104.34 kDa 
• Atom Count: 7,210 
• Modelled Residue Count: 908 
• Deposited Residue Count: 918 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STALKED-CELL DIFFERENTIATION CONTROLLING PROTEIN	A, B	459	Caulobacter vibrioides CB15	Mutation(s): 0  EC: 2.7.7.65
UniProt
Find proteins for B8GZM2 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore B8GZM2  Go to UniProtKB:  B8GZM2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5GP	PDBBind:  1W25	Ki: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.87	α = 90
b = 135.87	β = 90
c = 169.247	γ = 90

Software Package:

Software Name	Purpose
DM	model building
TRUNCATE	data scaling
SHELXD	phasing
SHARP	phasing
SOLOMON	phasing
DM	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-18 
Deposition Author(s): Chan, C., Schirmer, T., Jenal, U.

Revision History  

• Version 1.0: 2004-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Advisory, Data collection, Experimental preparation, Other
• Version 1.3: 2019-05-29
  Changes: Data collection, Other