3P2H

Crystal structure of TofI in a ternary complex with an inhibitor and MTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small-molecule inhibitor binding to an N-acyl-homoserine lactone synthase

Chung, J.Goo, E.Yu, S.Choi, O.Lee, J.Kim, J.Kim, H.Igarashi, J.Suga, H.Moon, J.S.Hwang, I.Rhee, S.

(2011) Proc.Natl.Acad.Sci.USA 108: 12089-12094

  • DOI: 10.1073/pnas.1103165108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quorum sensing (QS) controls certain behaviors of bacteria in response to population density. In gram-negative bacteria, QS is often mediated by N-acyl-L-homoserine lactones (acyl-HSLs). Because QS influences the virulence of many pathogenic bacteria ...

    Quorum sensing (QS) controls certain behaviors of bacteria in response to population density. In gram-negative bacteria, QS is often mediated by N-acyl-L-homoserine lactones (acyl-HSLs). Because QS influences the virulence of many pathogenic bacteria, synthetic inhibitors of acyl-HSL synthases might be useful therapeutically for controlling pathogens. However, rational design of a potent QS antagonist has been thwarted by the lack of information concerning the binding interactions between acyl-HSL synthases and their ligands. In the gram-negative bacterium Burkholderia glumae, QS controls virulence, motility, and protein secretion and is mediated by the binding of N-octanoyl-L-HSL (C8-HSL) to its cognate receptor, TofR. C8-HSL is synthesized by the acyl-HSL synthase TofI. In this study, we characterized two previously unknown QS inhibitors identified in a focused library of acyl-HSL analogs. Our functional and X-ray crystal structure analyses show that the first inhibitor, J8-C8, binds to TofI, occupying the binding site for the acyl chain of the TofI cognate substrate, acylated acyl-carrier protein. Moreover, the reaction byproduct, 5'-methylthioadenosine, independently binds to the binding site for a second substrate, S-adenosyl-L-methionine. Closer inspection of the mode of J8-C8 binding to TofI provides a likely molecular basis for the various substrate specificities of acyl-HSL synthases. The second inhibitor, E9C-3oxoC6, competitively inhibits C8-HSL binding to TofR. Our analysis of the binding of an inhibitor and a reaction byproduct to an acyl-HSL synthase may facilitate the design of a new class of QS-inhibiting therapeutic agents.


    Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AHL synthase
A
201Burkholderia glumaeMutation(s): 3 
Gene Names: tofI
EC: 2.3.1.184
Find proteins for Q4VSJ8 (Burkholderia glumae)
Go to UniProtKB:  Q4VSJ8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOO
Query on NOO

Download SDF File 
Download CCD File 
A
N-(3-oxocyclohex-1-en-1-yl)octanamide
C14 H23 N O2
USNFUKCPLYEHLS-UHFFFAOYSA-N
 Ligand Interaction
MTA
Query on MTA

Download SDF File 
Download CCD File 
A
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NOOKd: 3600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.100α = 90.00
b = 66.100β = 90.00
c = 104.200γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-10-02 
  • Released Date: 2011-07-06 
  • Deposition Author(s): Yu, S., Rhee, S.

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references