8X6U | pdb_00008x6u

Crystal structure of EfCDA in complex with dFdU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

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


Literature

Deciphering the role of Enterococcus faecium cytidine deaminase in gemcitabine resistance of gallbladder cancer.

Jiang, L.Zhang, L.Shu, Y.Zhang, Y.Gao, L.Qiu, S.Zhang, W.Dai, W.Chen, S.Huang, Y.Liu, Y.

(2024) J Biological Chem 300: 107171-107171

  • DOI: https://doi.org/10.1016/j.jbc.2024.107171
  • Primary Citation of Related Structures:  
    8X6U, 8X6W, 8X6Y

  • PubMed Abstract: 

    Gemcitabine-based chemotherapy is a cornerstone of standard care for gallbladder cancer (GBC) treatment. Still, drug resistance remains a significant challenge, influenced by factors such as tumor-associated microbiota impacting drug concentrations within tumors. Enterococcus faecium, a member of tumor-associated microbiota, was notably enriched in the GBC patient cluster. In this study, we investigated the biochemical characteristics, catalytic activity, and kinetics of the cytidine deaminase of E. faecium (EfCDA). EfCDA showed the ability to convert gemcitabine to its metabolite 2',2'-difluorodeoxyuridine. Both EfCDA and E. faecium can induce gemcitabine resistance in GBC cells. Moreover, we determined the crystal structure of EfCDA, in its apo form and in complex with 2', 2'-difluorodeoxyuridine at high resolution. Mutation of key residues abolished the catalytic activity of EfCDA and reduced the gemcitabine resistance in GBC cells. Our findings provide structural insights into the molecular basis for recognizing gemcitabine metabolite by a bacteria CDA protein and may provide potential strategies to combat cancer drug resistance and improve the efficacy of gemcitabine-based chemotherapy in GBC treatment.


  • Organizational Affiliation
    • School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China; Department of General Surgery, Shanghai Research Center of Biliary Tract Disease, Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EfCDA
A, B
134EnterococcusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.914α = 90
b = 82.914β = 90
c = 81.646γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171186
National Natural Science Foundation of China (NSFC)China31870741

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references