4WK6

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) (G141A) from Vibrio cholerae in complex with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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This is version 1.7 of the entry. See complete history


Literature

Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.

Hou, J.Zheng, H.Chruszcz, M.Zimmerman, M.D.Shumilin, I.A.Osinski, T.Demas, M.Grimshaw, S.Minor, W.

(2015) J Bacteriol 198: 463-476

  • DOI: https://doi.org/10.1128/JB.00360-15
  • Primary Citation of Related Structures:  
    3OP4, 3RRO, 3RSH, 3TZC, 3TZK, 3U09, 4I08, 4WJZ, 4WK6, 5END

  • PubMed Abstract: 

    β-Ketoacyl-(acyl carrier protein) reductase (FabG) catalyzes the key reductive reaction in the elongation cycle of fatty acid synthesis (FAS), which is a vital metabolic pathway in bacteria and a promising target for new antibiotic development. The activation of the enzyme is usually linked to the formation of a catalytic triad and cofactor binding, and crystal structures of FabG from different organisms have been captured in either the active or inactive conformation. However, the structural elements which enable activation of FabG require further exploration. Here we report the findings of structural, enzymatic, and binding studies of the FabG protein found in the causative agent of cholera, Vibrio cholerae (vcFabG). vcFabG exists predominantly as a dimer in solution and is able to self-associate to form tetramers, which is the state seen in the crystal structure. The formation of the tetramer may be promoted by the presence of the cofactor NADP(H). The transition between the dimeric and tetrameric states of vcFabG is related to changes in the conformations of the α4/α5 helices on the dimer-dimer interface. Two glycine residues adjacent to the dimer interface (G92 and G141) are identified to be the hinge for the conformational changes, while the catalytic tyrosine (Y155) and a glutamine residue that forms hydrogen bonds to both loop β4-α4 and loop β5-α5 (Q152) stabilize the active conformation. The functions of the aforementioned residues were confirmed by binding and enzymatic assays for the corresponding mutants. This paper describes the results of structural, enzymatic, and binding studies of FabG from Vibrio cholerae (vcFabG). In this work, we dissected the structural elements responsible for the activation of vcFabG. The structural information provided here is essential for the development of antibiotics specifically targeting bacterial FabG, especially for the multidrug-resistant strains of V. cholerae.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA Center for Structural Genomics of Infectious Diseases (CSGID)‡


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier protein] reductase
A, B, C, D
251Vibrio cholerae 12129(1)Mutation(s): 1 
Gene Names: VCG_002050
EC: 1.1.1.100
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.904α = 90
b = 110.337β = 90
c = 117.482γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272200700058C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2015-08-26
    Changes: Data collection
  • Version 1.2: 2015-11-25
    Changes: Database references
  • Version 1.3: 2016-02-03
    Changes: Database references
  • Version 1.4: 2017-09-27
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.6: 2022-04-13
    Changes: Database references, Structure summary
  • Version 1.7: 2023-12-27
    Changes: Data collection, Refinement description