Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 72.80 kDa 
• Atom Count: 4515 
• Modelled Residue Count: 543 
• Deposited Residue Count: 608 
• Unique protein chains: 1

4H54

Crystal structure of the diguanylate cyclase DgcZ

• PDB DOI: 10.2210/pdb4H54/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-09-18 Released: 2013-07-03 
• Deposition Author(s): Zaehringer, F., Schirmer, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.242 
• R-Value Observed: 0.242 

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

• PubMed: 23769666 
• DOI: 10.1016/j.str.2013.04.026
• Primary Citation of Related Structures:  
  3T9O, 3TVK, 4H54


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diguanylate cyclase YdeH	A, B	304	Escherichia coli K-12	Mutation(s): 1  Gene Names: b1535, JW1528, ydeG, ydeH, dgcZ EC: 2.7.7.65
UniProt
Find proteins for P31129 (Escherichia coli (strain K12)) Explore P31129  Go to UniProtKB:  P31129

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	G [auth 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) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N
GAV	D [auth A], F [auth A], I [auth B], K [auth B]	GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE C10 H16 N5 O13 P3 S YRUWXBKVSXSSGS-KIOICMOXSA-N
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.242 
• R-Value Observed: 0.242 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.593	α = 90
b = 102.593	β = 90
c = 129.156	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MARMOSAIC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-18 
• Released Date: 2013-07-03 
Deposition Author(s): Zaehringer, F., Schirmer, T.

Revision History  

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