Crystal structure of Apo PBP1a from Acinetobacter baumannii

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Distinctive attributes of beta-lactam target proteins in Acinetobacter baumannii relevant to development of new antibiotics

Han, S.Caspers, N.Zaniewski, R.P.Lacey, B.M.Tomaras, A.P.Feng, X.Geoghegan, K.F.Shanmugasundaram, V.

(2011) J Am Chem Soc 133: 20536-20545

  • DOI: https://doi.org/10.1021/ja208835z
  • Primary Citation of Related Structures:  
    3UDF, 3UDI, 3UDX, 3UE0, 3UE1, 3UE3

  • PubMed Abstract: 

    Multi-drug-resistant forms of the Gram-negative pathogen Acinetobacter baumannii are an emerging threat to human health and further complicate the general problem of treating serious bacterial infections. Meeting this challenge requires an improved understanding of the relationships between the structures of major therapeutic targets in this organism and the activity levels exhibited against it by different antibiotics. Here we report the first crystal structures of A. baumannii penicillin-binding proteins (PBPs) covalently inactivated by four β-lactam antibiotics. We also relate the results to kinetic, biophysical, and computational data. The structure of the class A protein PBP1a was solved in apo form and for its covalent conjugates with benzyl penicillin, imipenem, aztreonam, and the siderophore-conjugated monocarbam MC-1. It included a novel domain genetically spliced into a surface loop of the transpeptidase domain that contains three conserved loops. Also reported here is the first high-resolution structure of the A. baumannii class B enzyme PBP3 in apo form. Comparison of this structure with that of MC-1-derivatized PBP3 of Pseudomonas aeruginosa identified differences between these orthologous proteins in A. baumannii and P. aeruginosa. Thermodynamic analyses indicated that desolvation effects in the PBP3 ligand-binding sites contributed significantly to the thermal stability of the enzyme-antibiotic covalent complexes. Across a significant range of values, they correlated well with results from studies of inactivation kinetics and the protein structures. The structural, biophysical, and computational data help rationalize differences in the functional performance of antibiotics against different protein targets and can be used to guide the design of future agents.

  • Organizational Affiliation

    Pfizer Worldwide Research, Eastern Point Road, Groton, Connecticut 06340, USA. seungil.han@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 1a
A, B
731Acinetobacter baumanniiMutation(s): 0 
Gene Names: ponA
Find proteins for G1C794 (Acinetobacter baumannii)
Explore G1C794 
Go to UniProtKB:  G1C794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1C794
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.87α = 90
b = 243β = 90
c = 49.4γ = 90
Software Package:
Software NamePurpose
autoPROCdata collection
autoPROCdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2011-12-14 
  • Deposition Author(s): Han, S.

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description