4U65

Structure of the periplasmic output domain of the Legionella pneumophila LapD ortholog CdgS9 in complex with Pseudomonas fluorescens LapG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-GMP.

Chatterjee, D.Cooley, R.B.Boyd, C.D.Mehl, R.A.O'Toole, G.A.Sondermann, H.

(2014) Elife 3: e03650-e03650

  • DOI: 10.7554/eLife.03650
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Stable surface adhesion of cells is one of the early pivotal steps in bacterial biofilm formation, a prevalent adaptation strategy in response to changing environments. In Pseudomonas fluorescens, this process is regulated by the Lap system and the s ...

    Stable surface adhesion of cells is one of the early pivotal steps in bacterial biofilm formation, a prevalent adaptation strategy in response to changing environments. In Pseudomonas fluorescens, this process is regulated by the Lap system and the second messenger cyclic-di-GMP. High cytoplasmic levels of cyclic-di-GMP activate the transmembrane receptor LapD that in turn recruits the periplasmic protease LapG, preventing it from cleaving a cell surface-bound adhesin, thereby promoting cell adhesion. In this study, we elucidate the molecular basis of LapG regulation by LapD and reveal a remarkably sensitive switching mechanism that is controlled by LapD's HAMP domain. LapD appears to act as a coincidence detector, whereby a weak interaction of LapG with LapD transmits a transient outside-in signal that is reinforced only when cyclic-di-GMP levels increase. Given the conservation of key elements of this receptor system in many bacterial species, the results are broadly relevant for cyclic-di-GMP- and HAMP domain-regulated transmembrane signaling.


    Organizational Affiliation

    Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Two component histidine kinase, GGDEF domain protein/EAL domain protein
A, B, C, D
131Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Mutation(s): 0 
Find proteins for Q5ZXA3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Go to UniProtKB:  Q5ZXA3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative cystine protease
E, F
197Pseudomonas fluorescens (strain Pf0-1)Mutation(s): 0 
Gene Names: lapF
Find proteins for Q3KK32 (Pseudomonas fluorescens (strain Pf0-1))
Go to UniProtKB:  Q3KK32
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/94 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 75.854α = 90.00
b = 73.674β = 92.88
c = 88.223γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesDMR-1332208
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM-103485
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01- RAI097307
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32-GM108440
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32-GM08704
National Science Foundation (United States)United StatesMCB9984521

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-17
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Other, Source and taxonomy