6D6C

The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop "Out" Conformation for LasR.

O'Reilly, M.C.Dong, S.H.Rossi, F.M.Karlen, K.M.Kumar, R.S.Nair, S.K.Blackwell, H.E.

(2018) Cell Chem Biol 25: 1128-1139.e3

  • DOI: 10.1016/j.chembiol.2018.06.007
  • Primary Citation of Related Structures:  
    6D6A, 6D6B, 6D6C, 6D6D, 6D6L, 6D6M, 6D6N, 6D6O, 6D6P

  • PubMed Abstract: 
  • Chemical strategies to block quorum sensing (QS) could provide a route to attenuate virulence in bacterial pathogens. Considerable research has focused on this approach in Pseudomonas aeruginosa, which uses the LuxR-type receptor LasR to regulate much of its QS network ...

    Chemical strategies to block quorum sensing (QS) could provide a route to attenuate virulence in bacterial pathogens. Considerable research has focused on this approach in Pseudomonas aeruginosa, which uses the LuxR-type receptor LasR to regulate much of its QS network. Non-native ligands that antagonize LasR have been developed, yet we have little understanding of the mode by which these compounds interact with LasR and alter its function, as the receptor is unstable in their presence. Herein, we report an approach to circumvent this challenge through the study of a series of synthetic LasR agonists with varying levels of potency. Structural investigations of these ligands with the LasR ligand-binding domain reveal that certain agonists can enforce a conformation that deviates from that observed for other, often more potent agonists. These results, when combined with cell-based and biophysical analyses, suggest a functional model for LasR that could guide future ligand design.


    Organizational Affiliation

    Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA. Electronic address: blackwell@chem.wisc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional activator protein LasR
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
170Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lasRPA1430
UniProt
Find proteins for P25084 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P25084 
Go to UniProtKB:  P25084
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FYD (Subject of Investigation/LOI)
Query on FYD

Download Ideal Coordinates CCD File 
M [auth A] , N [auth B] , O [auth C] , P [auth D] , Q [auth E] , R [auth F] , S [auth G] , U [auth H] , 
M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], U [auth H], V [auth I], W [auth J], X [auth K], Y [auth L]
2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate
C22 H16 Br2 N2 O6
UJZBVAOLSMKIHH-UHFFFAOYSA-N
 Ligand Interaction
HIS (Subject of Investigation/LOI)
Query on HIS

Download Ideal Coordinates CCD File 
T [auth H]HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.409α = 90
b = 85.341β = 96.57
c = 232.465γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
UCSD-systemdata processing
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-04-20 
  • Released Date: 2018-08-08 
  • Deposition Author(s): Dong, S.H., Nair, S.K.

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references