5UJO

X-Ray Crystal Structure of Ruthenocenyl-7-Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with CTX-M-14 E166A Beta-Lactamase

  • Classification: HYDROLASE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2017-01-18 Released: 2017-02-08 
  • Deposition Author(s): Lewandowski, E.M., Chen, Y.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Polish National Science Centre

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Antibacterial Properties of Metallocenyl-7-ADCA Derivatives and Structure in Complex with CTX-Mbeta-Lactamase.

Lewandowski, E.M.Szczupak, L.Wong, S.Skiba, J.Guspiel, A.Solecka, J.Vrcek, V.Kowalski, K.Chen, Y.

(2017) Organometallics 36: 1673-1676

  • DOI: https://doi.org/10.1021/acs.organomet.6b00888
  • Primary Citation of Related Structures:  
    5UJO

  • PubMed Abstract: 

    A series of six novel metallocenyl-7-ADCA (metallocenyl = ferrocenyl or ruthenocenyl; 7-ADCA = 7-aminodesacetoxycephalosporanic acid) conjugates were synthesized and their antibacterial properties evaluated by biochemical and microbiological assays. The ruthenocene derivatives showed a higher level of inhibition of DD-carboxypeptidase 64-575, a Penicillin Binding Protein (PBP), than the ferrocene derivatives and the reference compound penicillin G. Protein X-ray crystallographic analysis revealed a covalent acyl-enzyme complex of a ruthenocenyl compound with CTX-M β-lactamase E166A mutant, corresponding to a similar complex with PBPs responsible for the bactericidal activities of these compounds. Most interestingly, an intact compound was captured at the crystal-packing interface, elucidating for the first time the structure of a metallocenyl β-lactam compound that previously eluded small molecule crystallography. We propose that protein crystals, even from biologically unrelated molecules, can be utilized to determine structures of small molecules.


  • Organizational Affiliation

    Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
263Escherichia coliMutation(s): 1 
Gene Names: blaCTX-MCTX-M-14
EC: 3.5.2.6
UniProt
Find proteins for Q9L5C8 (Escherichia coli)
Explore Q9L5C8 
Go to UniProtKB:  Q9L5C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L5C8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.961α = 90
b = 107.351β = 101.36
c = 47.956γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI03158
Polish National Science CentrePolandDEC-2013/11/B/ST5/00997

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description