4FOU

Structure of the PilZ-FimX(EAL domain)-c-di-GMP complex responsible for the regulation of bacterial Type IV pilus biogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the PilZ-FimXEAL-c-di-GMP Complex Responsible for the Regulation of Bacterial Type IV Pilus Biogenesis.

Guzzo, C.R.Dunger, G.Salinas, R.K.Farah, C.S.

(2013) J.Mol.Biol. 425: 2174-2197

  • DOI: 10.1016/j.jmb.2013.03.021
  • Primary Citation of Related Structures:  4FOJ, 4FOK

  • PubMed Abstract: 
  • Signal transduction pathways mediated by cyclic-bis(3'→5')-dimeric GMP (c-di-GMP) control many important and complex behaviors in bacteria. C-di-GMP is synthesized through the action of GGDEF domains that possess diguanylate cyclase activity and is d ...

    Signal transduction pathways mediated by cyclic-bis(3'→5')-dimeric GMP (c-di-GMP) control many important and complex behaviors in bacteria. C-di-GMP is synthesized through the action of GGDEF domains that possess diguanylate cyclase activity and is degraded by EAL or HD-GYP domains with phosphodiesterase activity. There is mounting evidence that some important c-di-GMP-mediated pathways require protein-protein interactions between members of the GGDEF, EAL, HD-GYP and PilZ protein domain families. For example, interactions have been observed between PilZ and the EAL domain from FimX of Xanthomonas citri (Xac). FimX and PilZ are involved in the regulation of type IV pilus biogenesis via interactions of the latter with the hexameric PilB ATPase associated with the bacterial inner membrane. Here, we present the crystal structure of the ternary complex made up of PilZ, the FimX EAL domain (FimXEAL) and c-di-GMP. PilZ interacts principally with the lobe region and the N-terminal linker helix of the FimXEAL. These interactions involve a hydrophobic surface made up of amino acids conserved in a non-canonical family of PilZ domains that lack intrinsic c-di-GMP binding ability and strand complementation that joins β-sheets from both proteins. Interestingly, the c-di-GMP binds to isolated FimXEAL and to the PilZ-FimXEAL complex in a novel conformation encountered in c-di-GMP-protein complexes in which one of the two glycosidic bonds is in a rare syn conformation while the other adopts the more common anti conformation. The structure points to a means by which c-di-GMP and PilZ binding could be coupled to FimX and PilB conformational states.


    Organizational Affiliation

    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo SP 05508-000, Brazil; Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo SP 05508-900, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FimX
A, B
264Xanthomonas axonopodis pv. citri (strain 306)N/A
Find proteins for Q8PJX9 (Xanthomonas axonopodis pv. citri (strain 306))
Go to UniProtKB:  Q8PJX9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Type IV fimbriae assembly protein
D, C
117Xanthomonas axonopodis pv. citri (strain 306)Gene Names: pilZ
Find proteins for Q8PND9 (Xanthomonas axonopodis pv. citri (strain 306))
Go to UniProtKB:  Q8PND9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download SDF File 
Download CCD File 
A, 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)
c-di-GMP, Cyclic diguanosine monophosphate
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.186 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 126.787α = 90.00
b = 126.787β = 90.00
c = 107.317γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references
  • Version 1.2: 2013-06-12
    Type: Database references