4RT1

Structure of the Alg44 PilZ domain (R95A mutant) from Pseudomonas aeruginosa PAO1 in complex with c-di-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dimeric c-di-GMP Is Required for Post-translational Regulation of Alginate Production in Pseudomonas aeruginosa.

Whitney, J.C.Whitfield, G.B.Marmont, L.S.Yip, P.Neculai, A.M.Lobsanov, Y.D.Robinson, H.Ohman, D.E.Howell, P.L.

(2015) J.Biol.Chem. 290: 12451-12462

  • DOI: 10.1074/jbc.M115.645051
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. Among the protei ...

    Pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. Among the proteins required for alginate production, Alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding activity post-translationally regulates alginate secretion. In this study, we report the 1.8 Å crystal structure of the cytoplasmic region of Alg44 in complex with dimeric self-intercalated c-di-GMP and characterize its dinucleotide-binding site using mutational analysis. The structure shows that the c-di-GMP binding region of Alg44 adopts a PilZ domain fold with a dimerization mode not previously observed for this family of proteins. Calorimetric binding analysis of residues in the c-di-GMP binding site demonstrate that mutation of Arg-17 and Arg-95 alters the binding stoichiometry between c-di-GMP and Alg44 from 2:1 to 1:1. Introduction of these mutant alleles on the P. aeruginosa chromosome show that the residues required for binding of dimeric c-di-GMP in vitro are also required for efficient alginate production in vivo. These results suggest that the dimeric form of c-di-GMP represents the biologically active signaling molecule needed for the secretion of an important virulence factor produced by P. aeruginosa.


    Organizational Affiliation

    the Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973-5000, and.,From the Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, howell@sickkids.ca.,From the Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,the Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center and McGuire Veterans Affairs Medical Center, Richmond, Virginia 23298-0678.,From the Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alginate biosynthesis protein Alg44
A, B, C
112Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 2 
Gene Names: alg44
EC: 2.4.1.33
Find proteins for Q9HY69 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HY69
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
C2E
Query on C2E

Download SDF File 
Download CCD File 
A, B, C
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
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C2EKd: 730 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 106.075α = 90.00
b = 106.075β = 90.00
c = 122.314γ = 120.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references