2R2D

Structure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens.

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

(2007) Biochemistry 46: 11789-11799

  • DOI: https://doi.org/10.1021/bi7012849
  • Primary Citation of Related Structures:  
    2R2D

  • PubMed Abstract: 

    N-Acyl-l-homoserine lactone (AHL) mediated quorum-sensing regulates virulence factor production in a variety of Gram-negative bacteria. Proteins capable of degrading these autoinducers have been called "quorum-quenching" enzymes, can block many quorum-sensing dependent phenotypes, and represent potentially useful reagents for clinical, agricultural, and industrial applications. The most characterized quorum-quenching enzymes to date are the AHL lactonases, which are metalloproteins that belong to the metallo-beta-lactamase superfamily. Here, we report the cloning, heterologous expression, purification, metal content, substrate specificity, and three-dimensional structure of AiiB, an AHL lactonase from Agrobacterium tumefaciens. Much like a homologous AHL lactonase from Bacillus thuringiensis, AiiB appears to be a metal-dependent AHL lactonase with broad specificity. A phosphate dianion is bound to the dinuclear zinc site and the active-site structure suggests specific mechanistic roles for an active site tyrosine and aspartate. To our knowledge, this is the second representative structure of an AHL lactonase and the first of an AHL lactonase from a microorganism that also produces AHL autoinducers. This work should help elucidate the hydrolytic ring-opening mechanism of this family of enzymes and also facilitate the design of more effective quorum-quenching catalysts.


  • Organizational Affiliation

    Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zn-dependent hydrolases
A, B, C, D, E
A, B, C, D, E, F
276Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: aiiB
UniProt
Find proteins for A9CKY2 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CKY2 
Go to UniProtKB:  A9CKY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CKY2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
FA [auth E]
I [auth A]
JA [auth F]
AA [auth D],
EA [auth E],
FA [auth E],
I [auth A],
JA [auth F],
O [auth B],
P [auth B],
U [auth C],
V [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D]
GA [auth E]
J [auth A]
K [auth A]
KA [auth F]
BA [auth D],
GA [auth E],
J [auth A],
K [auth A],
KA [auth F],
L [auth A],
Q [auth B],
R [auth B],
W [auth C],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth E]
DA [auth E]
G [auth A]
H [auth A]
HA [auth F]
CA [auth E],
DA [auth E],
G [auth A],
H [auth A],
HA [auth F],
IA [auth F],
M [auth B],
N [auth B],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.146α = 90
b = 158.033β = 104.48
c = 80.439γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2015-06-17
    Changes: Derived calculations
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations