4H54

Crystal structure of the diguanylate cyclase DgcZ

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure and signaling mechanism of a zinc-sensory diguanylate cyclase.

Zahringer, F., Lacanna, E., Jenal, U., Schirmer, T., Boehm, A.

(2013) Structure 21: 1149-1157

  • DOI: 10.1016/j.str.2013.04.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Diguanylate cyclases synthesize the second messenger c-di-GMP, which in turn governs a plethora of physiological processes in bacteria. Although most diguanylate cyclases harbor sensory domains, their input signals are largely unknown. Here, we demon ...

    Diguanylate cyclases synthesize the second messenger c-di-GMP, which in turn governs a plethora of physiological processes in bacteria. Although most diguanylate cyclases harbor sensory domains, their input signals are largely unknown. Here, we demonstrate that diguanylate cyclase DgcZ (YdeH) from Escherichia coli is regulated allosterically by zinc. Crystal structures show that the zinc ion is bound to the 3His/1Cys motif of the regulatory chemoreceptor zinc-binding domain, which mediates subunit contact within the dimeric enzyme. In vitro, zinc reversibly inhibits DgcZ with a subfemtomolar Ki constant. In vivo, bacterial biofilm formation is modulated by externally applied zinc in a DgcZ- and c-di-GMP-dependent fashion. The study outlines the structural principles of this zinc sensor. Zinc binding seems to regulate the activity of the catalytic GGDEF domains by impeding their mobility and thus preventing productive encounter of the two GTP substrates.

    Organizational Affiliation: 

    Focal Area of Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diguanylate cyclase YdeH
A, B
304Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: dgcZ (ydeG, ydeH)
EC: 2.7.7.65
Find proteins for P31129 (Escherichia coli (strain K12))
Go to UniProtKB:  P31129
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
C2E
Query on C2E
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Download CCD File 
A
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)
c-di-GMP; Cyclic diguanosine monophosphate
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GAV
Query on GAV
Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE
C10 H16 N5 O13 P3 S
YRUWXBKVSXSSGS-KIOICMOXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.242 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 102.593α = 90.00
b = 102.593β = 90.00
c = 129.156γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
BUSTERrefinement
MARMOSAICdata collection
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references