6CGZ

Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound to C6-AHL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Literature

Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties.

Bergonzi, C.Schwab, M.Naik, T.Daude, D.Chabriere, E.Elias, M.

(2018) Sci Rep 8: 11262-11262

  • DOI: https://doi.org/10.1038/s41598-018-28988-5
  • Primary Citation of Related Structures:  
    6CGY, 6CGZ, 6CH0

  • PubMed Abstract: 

    Quorum quenching lactonases are enzymes that are capable of disrupting bacterial signaling based on acyl homoserine lactones (AHL) via their enzymatic degradation. In particular, lactonases have therefore been demonstrated to inhibit bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. Here we characterized biochemically and structurally a novel representative from the metallo-β-lactamase superfamily, named AaL that was isolated from the thermoacidophilic bacterium Alicyclobacillus acidoterrestris. AaL is a potent quorum quenching enzyme as demonstrated by its ability to inhibit the biofilm formation of Acinetobacter baumannii. Kinetic studies demonstrate that AaL is both a proficient and a broad spectrum enzyme, being capable of hydrolyzing a wide range of lactones with high rates (k cat /K M  > 10 5  M -1 .s -1 ). Additionally, AaL exhibits unusually low K M values, ranging from 10 to 80 µM. Analysis of AaL structures bound to phosphate, glycerol, and C6-AHL reveals a unique hydrophobic patch (W26, F87 and I237), involved in substrate binding, possibly accounting for the enzyme's high specificity. Identifying the specificity determinants will aid the development of highly specific quorum quenching enzymes as potential therapeutics.


  • Organizational Affiliation

    Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B, C
282Alicyclobacillus acidoterrestris ATCC 49025Mutation(s): 0 
Gene Names: N007_09425
UniProt
Find proteins for T0BMH6 (Alicyclobacillus acidoterrestris (strain ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B))
Explore T0BMH6 
Go to UniProtKB:  T0BMH6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT0BMH6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HL6 (Subject of Investigation/LOI)
Query on HL6

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth B],
V [auth C]
N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide
C10 H17 N O3
ZJFKKPDLNLCPNP-QMMMGPOBSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
R [auth B],
W [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
U [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
M [auth B]
N [auth B]
S [auth C]
D [auth A],
E [auth A],
M [auth B],
N [auth B],
S [auth C],
T [auth C]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.94α = 90
b = 88.69β = 128.24
c = 97.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MnDriveUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Derived calculations
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations