8FQN

apo ADC-33 beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum.

Powers, R.A.June, C.M.Fernando, M.C.Fish, E.R.Maurer, O.L.Baumann, R.M.Beardsley, T.J.Taracila, M.A.Rudin, S.D.Hujer, K.M.Hujer, A.M.Santi, N.Villamil, V.Introvigne, M.L.Prati, F.Caselli, E.Bonomo, R.A.Wallar, B.J.

(2023) J Med Chem 66: 8510-8525

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00144
  • Primary Citation of Related Structures:  
    8FQM, 8FQN, 8FQO, 8FQP, 8FQQ, 8FQR, 8FQS, 8FQT, 8FQU, 8FQV, 8FQW

  • PubMed Abstract: 

    Class C Acinetobacter -derived cephalosporinases (ADCs) represent an important target for inhibition in the multidrug-resistant pathogen Acinetobacter baumannii . Many ADC variants have emerged, and characterization of their structural and functional differences is essential. Equally as important is the development of compounds that inhibit all prevalent ADCs despite these differences. The boronic acid transition state inhibitor, MB076 , a novel heterocyclic triazole with improved plasma stability, was synthesized and inhibits seven different ADC β-lactamase variants with K i values <1 μM. MB076 acted synergistically in combination with multiple cephalosporins to restore susceptibility. ADC variants containing an alanine duplication in the Ω-loop, specifically ADC-33, exhibited increased activity for larger cephalosporins, such as ceftazidime, cefiderocol, and ceftolozane. X-ray crystal structures of ADC variants in this study provide a structural context for substrate profile differences and show that the inhibitor adopts a similar conformation in all ADC variants, despite small changes near their active sites.


  • Organizational Affiliation

    Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamaseA [auth B],
B [auth A]
362Acinetobacter baumanniiMutation(s): 0 
Gene Names: ampCBAA1790NC_1053EP550_05490EP560_12590EQH48_05445
EC: 3.5.2.6
UniProt
Find proteins for A7Y407 (Acinetobacter baumannii)
Explore A7Y407 
Go to UniProtKB:  A7Y407
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7Y407
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.116α = 90
b = 83.551β = 90
c = 205.593γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
autoPROCdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI072219

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-07-26
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection