Crystal structure of FabD from Acinetobacter baumannii

Experimental Data Snapshot

  • Resolution: 1.67 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Elucidation of the crystal structure of FabD from the multidrug-resistant bacterium Acinetobacter baumannii.

Lee, W.C.Park, J.Balasubramanian, P.K.Kim, Y.

(2018) Biochem Biophys Res Commun 505: 208-214

  • DOI: https://doi.org/10.1016/j.bbrc.2018.09.079
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bacterial fatty acid synthesis (FAS) has been extensively studied as a potential target of antimicrobials. In FAS, FabD mediates transacylation of the malonyl group from malonyl-CoA to acyl-carrier protein (ACP). The mounting threat of nosocomial infection by multidrug-resistant Acinetobacter baumannii warrants a deeper understanding of its essential cellular mechanisms, which could lead to effective control of this highly competent pathogen. The molecular mechanisms involved in A. baumannii FAS are poorly understood, and recent research has suggested that Pseudomonas aeruginosa, a closely related nosocomial pathogen of A. baumannii, utilizes FAS to produce virulence factors. In this study, we solved the crystal structure of A. baumannii FabD (AbFabD) to provide a platform for the development of new antibacterial agents. Analysis of the structure of AbFabD confirmed the presence of highly conserved active site residues among bacterial homologs. Binding constants between AbFabD variants and A. baumannii ACP (AbACP) revealed critical conserved residues Lys195 and Lys200 involved in AbACP binding. Computational docking of a potential inhibitor, trifluoperazine, revealed a unique inhibitor-binding pocket near the substrate-binding site. The structural study presented herein will be useful for the structure-based design of potent AbFabD inhibitors.

  • Organizational Affiliation

    Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malonyl CoA-acyl carrier protein transacylase314Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
Find proteins for V5VFX0 (Acinetobacter baumannii)
Explore V5VFX0 
Go to UniProtKB:  V5VFX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5VFX0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.67 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.459α = 90
b = 67.459β = 90
c = 110.296γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic OfMSIP-2016R1A2B2008543

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references