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 
  • R-Value Observed: 0.131 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1021/acs.biochem.5b00499
  • Primary Citation of Related Structures:  
    4ZO2, 4ZO3

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acylhomoserine lactonase
A, B
294Chryseobacterium sp. StRB126Mutation(s): 0 
Gene Names: aidCCHSO_3121
UniProt
Find proteins for I7HB71 (Chryseobacterium sp. StRB126)
Explore I7HB71 
Go to UniProtKB:  I7HB71
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7HB71
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.257α = 90
b = 97.88β = 90
c = 110.871γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description