2BR6 | pdb_00002br6

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 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1073/pnas.0504996102
  • Primary Citation 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 28.91 kDa 
  • Atom Count: 2,157 
  • Modeled Residue Count: 240 
  • Deposited Residue Count: 252 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AIIA-LIKE PROTEIN252Bacillus 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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.220 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
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
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other