8R2Q | pdb_00008r2q

Mycobacterium tuberculosis fatty acyl CoA synthetase, FadD5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.238 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural enzymological studies of the long chain fatty acyl-CoA synthetase FadD5 from the mce1 operon of Mycobacterium tuberculosis.

Rahman, M.A.Dalwani, S.Venkatesan, R.

(2025) Biochem Biophys Res Commun 769: 151960-151960

  • DOI: https://doi.org/10.1016/j.bbrc.2025.151960
  • Primary Citation of Related Structures:  
    8R2Q, 8R2R

  • PubMed Abstract: 

    The cell wall of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is rich in complex lipids. During intracellular stage, Mtb depends on lipids for its survival. Mammalian cell entry (Mce) 1 complex encoded by the mce1 operon is a mycolic/fatty acid importer. mce1 operon also encodes a putative fatty acyl-CoA synthetase (FadD5; Rv0166), potentially responsible for the activation of fatty acids imported through the Mce1 complex by conjugating them to Coenzyme A. Here, we report that FadD5 is associated to membrane although it can be purified as a soluble dimeric protein. ATP and CoA binding influence FadD5's stability and conformation respectively. Enzymatic studies with fatty acids of varying chain lengths show that FadD5 prefers long chain fatty acids as substrates. X-ray crystallographic studies on FadD5 and its variant reveal that the C-terminal domain (∼100 residues) is cleaved off during crystallization. Noteworthy, deletion of this domain renders FadD5 completely inactive. SAXS studies, however, confirm the presence of full length FadD5 as a dimer in solution. Further structural analysis and comparisons with homologs provide insights on the possible mode of membrane association and fatty acyl tail binding.


  • Organizational Affiliation
    • Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable fatty-acid-CoA ligase FadD5 (Fatty-acid-CoA synthetase) (Fatty-acid-CoA synthase)
A, B
570Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fadD5
UniProt
Find proteins for O07411 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O07411 
Go to UniProtKB:  O07411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07411
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.238 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.914α = 90
b = 120.914β = 90
c = 247.915γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union713606
Academy of FinlandFinland332967
Other privateSigrid Juselius Foundation
Other privateTampere Tuberculosis Foundation
Other governmentUniversity of Oulu
Jane and Aatos Erkko FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references