7L5F

Crystal Structure of N-(2-oxocyclobutyl) decanamide Bound AiiA-Co


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Cyclobutanone Inhibitor of Cobalt-Functionalized Metallo-gamma-Lactonase AiiA with Cyclobutanone Ring Opening in the Active Site.

Reidl, C.T.Mascarenhas, R.Mohammad, T.S.H.Lutz Jr., M.R.Thomas, P.W.Fast, W.Liu, D.Becker, D.P.

(2021) ACS Omega 6: 13567-13578

  • DOI: https://doi.org/10.1021/acsomega.0c06348
  • Primary Citation of Related Structures:  
    7L5F

  • PubMed Abstract: 

    An α-amido cyclobutanone possessing a C10 hydrocarbon tail was designed as a potential transition-state mimetic for the quorum-quenching metallo-γ-lactonase autoinducer inactivator A (AiiA) with the support of in-house modeling techniques and found to be a competitive inhibitor of dicobalt(II) AiiA with an inhibition constant of K i = 0.007 ± 0.002 mM. The catalytic mechanism of AiiA was further explored using our product-based transition-state modeling (PBTSM) computational approach, providing substrate-intermediate models arising during enzyme turnover and further insight into substrate-enzyme interactions governing native substrate catalysis. These interactions were targeted in the docking of cyclobutanone hydrates into the active site of AiiA. The X-ray crystal structure of dicobalt(II) AiiA cocrystallized with this cyclobutanone inhibitor unexpectedly revealed an N -(2-oxocyclobutyl)decanamide ring-opened acyclic product bound to the enzyme active site (PDB 7L5F). The C10 alkyl chain and its interaction with the hydrophobic phenylalanine clamp region of AiiA adjacent to the active site enabled atomic placement of the ligand atoms, including the C10 alkyl chain. A mechanistic hypothesis for the ring opening is proposed involving a radical-mediated process.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acyl homoserine lactonase AiiA250Bacillus subtilisMutation(s): 0 
Gene Names: aiiA
EC: 3.1.1.81
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.699α = 90
b = 55.662β = 90
c = 80.582γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
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: 2021-07-28
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description