A Novel Interaction Mode between a Microbial GGDEF Domain and the Bis-(3, 5 )-cyclic di-GMP

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 

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The structure and inhibition of a GGDEF diguanylate cyclase complexed with (c-di-GMP)(2) at the active site

Yang, C.-Y.Chin, K.-H.Chuah, M.L.-C.Liang, Z.-X.Wang, A.H.-J.Chou, S.-H.

(2011) Acta Crystallogr D Biol Crystallogr 67: 997-1008

  • DOI: https://doi.org/10.1107/S090744491104039X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cyclic diguanosine monophosphate (c-di-GMP) is a key signalling molecule involved in regulating many important biological functions in bacteria. The synthesis of c-di-GMP is catalyzed by the GGDEF-domain-containing diguanylate cyclase (DGC), the activity of which is regulated by the binding of product at the allosteric inhibitory (I) site. However, a significant number of GGDEF domains lack the RxxD motif characteristic of the allosteric I site. Here, the structure of XCC4471(GGDEF), the GGDEF domain of a DGC from Xanthomonas campestris, in complex with c-di-GMP has been solved. Unexpectedly, the structure of the complex revealed a GGDEF-domain dimer cross-linked by two molecules of c-di-GMP at the strongly conserved active sites. In the complex (c-di-GMP)(2) adopts a novel partially intercalated form, with the peripheral guanine bases bound to the guanine-binding pockets and the two central bases stacked upon each other. Alteration of the residues involved in specific binding to c-di-GMP led to dramatically reduced K(d) values between XCC4471(GGDEF) and c-di-GMP. In addition, these key residues are strongly conserved among the many thousands of GGDEF-domain sequences identified to date. These results indicate a new product-bound form for GGDEF-domain-containing proteins obtained via (c-di-GMP)(2) binding at the active site. This novel XCC4471(GGDEF)-c-di-GMP complex structure may serve as a general model for the design of lead compounds to block the DGC activity of GGDEF-domain-containing proteins in X. campestris or other microorganisms that contain multiple GGDEF-domain proteins.

  • Organizational Affiliation

    Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Response regulator
A, B
167Xanthomonas campestris pv. campestrisMutation(s): 0 
Gene Names: XCC3486
Find proteins for Q8P559 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25))
Explore Q8P559 
Go to UniProtKB:  Q8P559
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8P559
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C2E

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
C20 H24 N10 O14 P2
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B]
C4 H10 O3
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
C2E PDBBind:  3QYY Kd: 8260 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.281α = 90
b = 87.281β = 90
c = 87.86γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Structure summary