2BR6

Crystal Structure of Quorum-Quenching N-Acyl Homoserine Lactone Lactonase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Molecular Structure and Catalytic Mechanism of a Quorum-Quenching N-Acyl-L-Homoserine Lactone Hydrolase.

Kim, M.H.Choi, W.C.Kang, H.O.Lee, J.S.Kang, B.S.Kim, K.J.Derewenda, Z.S.Oh, T.K.Lee, C.H.Lee, J.K.

(2005) Proc Natl Acad Sci U S A 102: 17606

  • DOI: 10.1073/pnas.0504996102
  • Primary Citation of Related Structures:  
    2BR6, 2BTN

  • PubMed Abstract: 
  • In many Gram-negative bacteria, including a number of pathogens such as Pseudomonas aeruginosa and Erwinia carotovora, virulence factor production and biofilm formation are linked to the quorum-sensing systems that use diffusible N-acyl-L-homoserine lactones (AHLs) as intercellular messenger molecules ...

    In many Gram-negative bacteria, including a number of pathogens such as Pseudomonas aeruginosa and Erwinia carotovora, virulence factor production and biofilm formation are linked to the quorum-sensing systems that use diffusible N-acyl-L-homoserine lactones (AHLs) as intercellular messenger molecules. A number of organisms also contain genes coding for lactonases that hydrolyze AHLs into inactive products, thereby blocking the quorum-sensing systems. Consequently, these enzymes attract intense interest for the development of antiinfection therapies. However, the catalytic mechanism of AHL-lactonase is poorly understood and subject to controversy. We here report a 2.0-angstroms resolution structure of the AHL-lactonase from Bacillus thuringiensis and a 1.7-angstroms crystal structure of its complex with L-homoserine lactone. Despite limited sequence similarity, the enzyme shows remarkable structural similarities to glyoxalase II and RNase Z proteins, members of the metallo-beta-lactamase superfamily. We present experimental evidence that AHL-lactonase is a metalloenzyme containing two zinc ions involved in catalysis, and we propose a catalytic mechanism for bacterial metallo-AHL-lactonases.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of Bacillus Thuringiensis Ahl-Lactonase.
      Kim, M.H., Kang, H.O., Kang, B.S., Kim, K.J., Choi, W.C., Oh, T.K., Lee, C.H., Lee, J.K.
      (2005) Biochim Biophys Acta 1750: 5

    Organizational Affiliation

    Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejon 305-600, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AIIA-LIKE PROTEINA252Bacillus thuringiensisMutation(s): 0 
EC: 3.1.1.81
UniProt
Find proteins for P0CJ63 (Bacillus thuringiensis subsp. kurstaki)
Explore P0CJ63 
Go to UniProtKB:  P0CJ63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CJ63
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HSL
Query on HSL

Download Ideal Coordinates CCD File 
F [auth A]HOMOSERINE LACTONE
C4 H7 N O2
QJPWUUJVYOJNMH-VKHMYHEASA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HSL PDBBind:  2BR6 Ki: 1.10e+6 (nM) from 1 assay(s)
Binding MOAD:  2BR6 Ki: 1.10e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.904α = 90
b = 55.745β = 90
c = 73.855γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance