3UE0

Crystal structure of Acinetobacter baumannii PBP1a in complex with Aztreonam

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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Literature

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: 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 ...

    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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein 1aA, B731Acinetobacter baumanniiMutation(s): 0 
Gene Names: ponA
EC: 2.4.1.129 (UniProt), 3.4.16.4 (UniProt)
UniProt
Find proteins for G1C794 (Acinetobacter baumannii)
Explore G1C794 
Go to UniProtKB:  G1C794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1C794
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZR
Query on AZR
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S,3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid
C13 H19 N5 O8 S2
OEVQTUTXOVDNJO-GEEOIBTQSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.08α = 90
b = 242.57β = 90
c = 49.31γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2011-10-28 
  • 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