4R8E | pdb_00004r8e

Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural Characterisation of the Beta-Ketoacyl-Acyl Carrier Protein Synthases, FabF and FabH, of Yersinia pestis.

Nanson, J.D.Himiari, Z.Swarbrick, C.M.Forwood, J.K.

(2015) Sci Rep 5: 14797-14797

  • DOI: https://doi.org/10.1038/srep14797
  • Primary Citation Related Structures: 
    4R8E, 4YLT, 4Z19

  • PubMed Abstract: 

    Yersinia pestis, the causative agent of bubonic, pneumonic, and septicaemic plague, remains a major public health threat, with outbreaks of disease occurring in China, Madagascar, and Peru in the last five years. The existence of multidrug resistant Y. pestis and the potential of this bacterium as a bioterrorism agent illustrates the need for new antimicrobials. The β-ketoacyl-acyl carrier protein synthases, FabB, FabF, and FabH, catalyse the elongation of fatty acids as part of the type II fatty acid biosynthesis (FASII) system, to synthesise components of lipoproteins, phospholipids, and lipopolysaccharides essential for bacterial growth and survival. As such, these enzymes are promising targets for the development of novel therapeutic agents. We have determined the crystal structures of the Y. pestis β-ketoacyl-acyl carrier protein synthases FabF and FabH, and compared these with the unpublished, deposited structure of Y. pestis FabB. Comparison of FabB, FabF, and FabH provides insights into the substrate specificities of these enzymes, and investigation of possible interactions with known β-ketoacyl-acyl carrier protein synthase inhibitors suggests FabB, FabF and FabH may be targeted simultaneously to prevent synthesis of the fatty acids necessary for growth and survival.


  • Organizational Affiliation
    • School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia.

Macromolecule Content 

  • Total Structure Weight: 86.46 kDa 
  • Atom Count: 6,041 
  • Modeled Residue Count: 822 
  • Deposited Residue Count: 826 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase 2
A, B
413Yersinia pestisMutation(s): 0 
Gene Names: fabFfabF4y1760YP_2253YPO1601
EC: 2.3.1.179
UniProt
Find proteins for A0A2S9PBT6 (Yersinia pestis)
Explore A0A2S9PBT6 
Go to UniProtKB:  A0A2S9PBT6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S9PBT6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.67α = 90
b = 63.91β = 107.14
c = 89.29γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references