4ZO2

AidC, a Dizinc Quorum-Quenching Lactonase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase with Atypical Selectivity.

Mascarenhas, R.Thomas, P.W.Wu, C.X.Nocek, B.P.Hoang, Q.Q.Liu, D.Fast, W.

(2015) Biochemistry 54: 4342-4353

  • DOI: 10.1021/acs.biochem.5b00499
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and ...

    Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 10(6) M(-1) s(-1) for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. Implications for the catalytic mechanism of AHL lactonases are discussed.


    Organizational Affiliation

    §Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acylhomoserine lactonase
A, B
294Chryseobacterium sp. StRB126Mutation(s): 0 
Gene Names: aidC
Find proteins for I7HB71 (Chryseobacterium sp. StRB126)
Go to UniProtKB:  I7HB71
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.257α = 90.00
b = 97.880β = 90.00
c = 110.871γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE-1308672
Robert A. Welch FoundationUnited StatesF-1572
Loyola University ChicagoUnited States--

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-29
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2017-11-22
    Type: Refinement description