3P2H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.231 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MTAClick on this verticalbar to view detailsBest fitted NOOClick on this verticalbar to view details

This is version 1.3 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 U S A 108: 12089-12094

  • DOI: https://doi.org/10.1073/pnas.1103165108
  • Primary Citation of Related Structures:  
    3P2F, 3P2H

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AHL synthase201Burkholderia glumaeMutation(s): 3 
Gene Names: tofI
EC: 2.3.1.184
UniProt
Find proteins for Q4VSJ8 (Burkholderia glumae (strain BGR1))
Explore Q4VSJ8 
Go to UniProtKB:  Q4VSJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4VSJ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA

Download Ideal Coordinates CCD File 
B [auth A]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
NOO
Query on NOO

Download Ideal Coordinates CCD File 
C [auth A]N-(3-oxocyclohex-1-en-1-yl)octanamide
C14 H23 N O2
USNFUKCPLYEHLS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.231 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.1α = 90
b = 66.1β = 90
c = 104.2γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MTAClick on this verticalbar to view detailsBest fitted NOOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations