1RAK

Bacterial cytosine deaminase D314S mutant bound to 5-fluoro-4-(S)-hydroxyl-3,4-dihydropyrimidine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy.

Mahan, S.D.Ireton, G.C.Knoeber, C.Stoddard, B.L.Black, M.E.

(2004) Protein Eng.Des.Sel. 17: 625-633

  • DOI: 10.1093/protein/gzh074
  • Primary Citation of Related Structures:  1R9X, 1R9Y, 1R9Z, 1RA0, 1RA5

  • PubMed Abstract: 
  • Cytosine deaminase (CD) is currently being used as a suicide gene for cancer gene therapy. The premise of this therapy is the preferential deamination of 5-fluorocytosine (5FC) to 5-fluorouracil by cancer cells expressing cytosine deaminase. However, ...

    Cytosine deaminase (CD) is currently being used as a suicide gene for cancer gene therapy. The premise of this therapy is the preferential deamination of 5-fluorocytosine (5FC) to 5-fluorouracil by cancer cells expressing cytosine deaminase. However, a lack of efficient gene transfer to tumors combined with inefficient 5FC turnover currently limits the clinical applications of this gene therapy approach. We have used random mutagenesis to create novel bacterial cytosine deaminases that demonstrate an increased preference for 5FC over cytosine. Among the 15 mutants isolated, one conferred sensitivity to Escherichia coli in a negative selection system at a concentration of 5FC that was 10-fold lower than a sublethal dose for wild-type CD. Evaluation of individual substitutions found in this double mutant (Q102R, D314G) demonstrated that the substitution at residue D314 was solely responsible for the observed increase in sensitivity to 5FC. Additional mutagenesis at D314 resulted in the identification of two more substitutions with the ability to confer enhanced 5FC sensitivity to E.coli. Structure determinations of the three CD variants in the presence and absence of a transition state 5FC analogue provide insights to the determinants of substrate binding specificity at the 5' position of the pyrimidine ring. CD mutant D314A is a promising candidate for further gene therapy studies.


    Organizational Affiliation

    Department of Pharmaceutical Sciences and the School of Molecular Biosciences, PO Box 646534, Washington State University, Pullman, WA 99164-6534, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytosine deaminase
A
430Escherichia coli (strain K12)Gene Names: codA
EC: 3.5.4.1, 3.5.4.-
Find proteins for P25524 (Escherichia coli (strain K12))
Go to UniProtKB:  P25524
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
FPY
Query on FPY

Download SDF File 
Download CCD File 
A
(4S)-5-FLUORO-4-HYDROXY-3,4-DIHYDROPYRIMIDIN-2(1H)-ONE
5-FLUORO-4-(S)-HYDROXY-3,4-DIHYDROPYRIMIDINE
C4 H5 F N2 O2
PRVUBDAKZJCBTI-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.172 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 109.481α = 90.00
b = 109.481β = 90.00
c = 241.088γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance