8XIJ | pdb_00008xij

Structure of acyltransferase GWT1 bound to palmitoyl-CoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the inhibition mechanism of fungal GWT1 by manogepix.

Dai, X.Liu, X.Li, J.Chen, H.Yan, C.Li, Y.Liu, H.Deng, D.Wang, X.

(2024) Nat Commun 15: 9194-9194

  • DOI: https://doi.org/10.1038/s41467-024-53512-x
  • Primary Citation of Related Structures:  
    8XIJ, 8XIK

  • PubMed Abstract: 

    Glycosylphosphatidylinositol (GPI) acyltransferase is crucial for the synthesis of GPI-anchored proteins. Targeting the fungal glycosylphosphatidylinositol acyltransferase GWT1 by manogepix is a promising antifungal strategy. However, the inhibitory mechanism of manogepix remains unclear. Here, we present cryo-EM structures of yeast GWT1 bound to the substrate (palmitoyl-CoA) and inhibitor (manogepix) at 3.3 Å and 3.5 Å, respectively. GWT1 adopts a unique fold with 13 transmembrane (TM) helixes. The palmitoyl-CoA inserts into the chamber among TM4, 5, 6, 7, and 12. The crucial residues (D145 and K155) located on the loop between TM4 and TM5 potentially bind to the GPI precursor, contributing to substrate recognition and catalysis, respectively. The antifungal drug, manogepix, occupies the hydrophobic cavity of the palmitoyl-CoA binding site, suggesting a competitive inhibitory mechanism. Structural analysis of resistance mutations elucidates the drug specificity and selectivity. These findings pave the way for the development of potent and selective antifungal drugs targeting GWT1.


  • Organizational Affiliation
    • Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GPI-anchored wall transfer protein 1490Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GWT1
EC: 2.3
Membrane Entity: Yes 
UniProt
Find proteins for P47026 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47026 
Go to UniProtKB:  P47026
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47026
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PKZ (Subject of Investigation/LOI)
Query on PKZ

Download Ideal Coordinates CCD File 
B [auth A]Palmitoyl-CoA
C37 H66 N7 O17 P3 S
MNBKLUUYKPBKDU-BBECNAHFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection