9K1K | pdb_00009k1k

Yeast Cytosine Deaminase mutant-M100H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.144 (Depositor), 0.145 (DCC) 
  • R-Value Work: 
    0.127 (Depositor), 0.127 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An engineered yeast cytosine deaminase with improved catalytic activity and stability for macrophage-mediated enzyme/prodrug therapy.

Zheng, J.Zhou, J.Yung, K.W.Y.Hu, Q.Lee, M.M.Chan, M.K.

(2025) Commun Biol 8: 1562-1562

  • DOI: https://doi.org/10.1038/s42003-025-08931-x
  • Primary Citation of Related Structures:  
    9K1K

  • PubMed Abstract: 

    Utilization of yeast cytosine deaminase (yCD) to activate the prodrug 5-fluorocytosine (5-FC) to 5-fluorouracil (5-FU) at the target site is an attractive strategy for overcoming the narrow therapeutic index of 5-FU. Nevertheless, protein delivery of yCD is challenging in part due to its thermal instability. Herein, we have rationally engineered a mutant yCD by replacing Met100 situated at the active site entry with the bulkier histidine to hinder potential oxidation of the active site Cys91. The engineered yCD-Met100His exhibits significantly enhanced activity and thermal stability. yCD-M100H is then genetically fused to the crystal-forming protein Cry3Aa to generate Cry3Aa-yCD-M100H fusion crystals to facilitate the enzyme's uptake into macrophages. The resulting Cry3Aa-yCD-M100H-loaded macrophages exhibit excellent penetration into tumor spheroids and readily convert 5-FC to 5-FU leading to efficacious cancer cell killing. This study showcases a promising route for stabilizing yCD and the feasibility of enzyme-internalized macrophages to serve as tumor-specific enzyme/prodrug activators.


  • Organizational Affiliation
    • School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosine deaminase
A, B
158Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: FCY1YPR062WYP9499.17
EC: 3.5.4.1
UniProt
Find proteins for Q12178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12178 
Go to UniProtKB:  Q12178
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12178
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.144 (Depositor), 0.145 (DCC) 
  • R-Value Work:  0.127 (Depositor), 0.127 (DCC) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.077α = 90
b = 79.077β = 90
c = 55.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong KongAoE/P-705/16

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references