8IVI

crystal structure of a medium-long chain fatty acyl-CoA ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural study of medium-long chain fatty acyl-CoA ligase FadD8 from Mycobacterium tuberculosis.

Li, S.Qu, Y.

(2023) Biochem Biophys Res Commun 672: 65-71

  • DOI: https://doi.org/10.1016/j.bbrc.2023.06.024
  • Primary Citation of Related Structures:  
    8IVI

  • PubMed Abstract: 

    In mycobacteria, lipids are important components of the cell wall and play a critical role for pathogenic activities. Lipids need to be activated before participating in many biological pathways. FadD proteins are members of the adenylate-forming superfamily, catalyzing activation of fatty acids. FadD8 is one of the 34 Mycobacterium tuberculosis FadD proteins, which was reported to be a putative medium-long chain fatty acyl-CoA ligase. Previous studies showed FadD8 from Mycobacterium smegmatis exhibited higher activity with oxidized cholesterol than fatty acids. However, the catalytic mechanism of the FadD8 is still exclusive. Here, we reported the crystal structure of FadD8 from Mycobacterium tuberculosis, which forms homodimer. Structural analysis revealed presence of a relatively narrow pocket compared to other FadD proteins and a novel alternative pocket, implying distinct substrate binding preference. We propose that FadD8 plays a vital role in cholesterol utilization and metabolism by catalyzing activation of cholesterol. Collectively, our findings provide novel information for the further studies of the inhibitor and drug development.


  • Organizational Affiliation

    Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, People's Republic of China. Electronic address: lishanshan9001@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Medium/long-chain-fatty-acid--CoA ligase FadD8
A, B
591Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fadD8Rv0551c
EC: 6.2.1.2 (PDB Primary Data), 6.2.1.3 (PDB Primary Data)
UniProt
Find proteins for O06417 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06417 
Go to UniProtKB:  O06417
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06417
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.23α = 90
b = 105β = 90
c = 135.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHASERphasing
xia2data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-02-14 
  • Deposition Author(s): Li, S.

Funding OrganizationLocationGrant Number
Health Commission of Henan ProvinceChinaLHGJ20190242

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release