3DHC

1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to The catalytic Metal Center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures.

Liu, D.Momb, J.Thomas, P.W.Moulin, A.Petsko, G.A.Fast, W.Ringe, D.

(2008) Biochemistry 47: 7706-7714

  • DOI: https://doi.org/10.1021/bi800368y
  • Primary Citation of Related Structures:  
    3DHA, 3DHB, 3DHC

  • PubMed Abstract: 

    Enzymes capable of hydrolyzing N-acyl- l-homoserine lactones (AHLs) used in some bacterial quorum-sensing pathways are of considerable interest for their ability to block undesirable phenotypes. Most known AHL hydrolases that catalyze ring opening (AHL lactonases) are members of the metallo-beta-lactamase enzyme superfamily and rely on a dinuclear zinc site for catalysis and stability. Here we report the three-dimensional structures of three product complexes formed with the AHL lactonase from Bacillus thuringiensis. Structures of the lactonase bound with two different concentrations of the ring-opened product of N-hexanoyl- l-homoserine lactone are determined at 0.95 and 1.4 A resolution and exhibit different product configurations. A structure of the ring-opened product of the non-natural N-hexanoyl- l-homocysteine thiolactone at 1.3 A resolution is also determined. On the basis of these product-bound structures, a substrate-binding model is presented that differs from previous proposals. Additionally, the proximity of the product to active-site residues and observed changes in protein conformation and metal coordination provide insight into the catalytic mechanism of this quorum-quenching metalloenzyme.


  • Organizational Affiliation

    Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-Acyl Homoserine Lactone Hydrolase254Bacillus thuringiensis serovar kurstakiMutation(s): 0 
Gene Names: aiiA
EC: 3.1.1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYK
Query on CYK

Download Ideal Coordinates CCD File 
D [auth A]N-hexanoyl-L-homocysteine
C10 H19 N O3 S
HAUWXQBEWNVHPD-QMMMGPOBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.775α = 90
b = 55.46β = 90
c = 79.191γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description