5XGE

Crystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseudomonas aeruginosa in complex with cyclic di-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa.

Liu, C.Liew, C.W.Wong, Y.H.Tan, S.T.Poh, W.H.Manimekalai, M.S.S.Rajan, S.Xin, L.Liang, Z.X.Gruber, G.Rice, S.A.Lescar, J.

(2018) J. Bacteriol. 200: --

  • DOI: 10.1128/JB.00515-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RbdA is a positive <i>r </i>egulator of <i>b </i>iofilm <i>d </i>ispersal of <i>Pseudomonas aeruginosa </i> Its cytoplasmic region (cRbdA) comprises an N-terminal Per-ARNT-Sim (PAS) domain followed by a diguanylate cyclase (GGDEF) domain and an E ...

    RbdA is a positive r egulator of b iofilm d ispersal of Pseudomonas aeruginosa Its cytoplasmic region (cRbdA) comprises an N-terminal Per-ARNT-Sim (PAS) domain followed by a diguanylate cyclase (GGDEF) domain and an EAL domain, whose phosphodiesterase activity is allosterically stimulated by GTP binding to the GGDEF domain. We report crystal structures of cRbdA and of two binary complexes: one with GTP/Mg 2+ bound to the GGDEF active site and one with the EAL domain bound to the c-di-GMP substrate. These structures unveil a 2-fold symmetric dimer stabilized by a closely packed N-terminal PAS domain and a noncanonical EAL dimer. The autoinhibitory switch is formed by an α-helix (S-helix) immediately N-terminal to the GGDEF domain that interacts with the EAL dimerization helix (α 6-E ) of the other EAL monomer and maintains the protein in a locked conformation. We propose that local conformational changes in cRbdA upon GTP binding lead to a structure with the PAS domain and S-helix shifted away from the GGDEF-EAL domains, as suggested by small-angle X-ray scattering (SAXS) experiments. Domain reorientation should be facilitated by the presence of an α-helical lever (H-helix) that tethers the GGDEF and EAL regions, allowing the EAL domain to rearrange into an active dimeric conformation. IMPORTANCE Biofilm formation by bacterial pathogens increases resistance to antibiotics. RbdA positively regulates biofilm dispersal of Pseudomonas aeruginosa The crystal structures of the cytoplasmic region of the RbdA protein presented here reveal that two evolutionarily conserved helices play an important role in regulating the activity of RbdA, with implications for other GGDEF-EAL dual domains that are abundant in the proteomes of several bacterial pathogens. Thus, this work may assist in the development of small molecules that promote bacterial biofilm dispersal.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore rscott@ntu.edu.sg julien@ntu.edu.sg.,Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein PA0861
A
568Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Find proteins for Q9I580 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I580
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download SDF File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.180 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 134.881α = 90.00
b = 134.881β = 90.00
c = 211.224γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Database references
  • Version 1.2: 2018-04-04
    Type: Data collection, Database references
  • Version 1.3: 2019-04-03
    Type: Data collection, Database references