1P6O

The crystal structure of yeast cytosine deaminase bound to 4(R)-hydroxyl-3,4-dihydropyrimidine at 1.14 angstroms.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The 1.14 a crystal structure of yeast Cytosine deaminase. Evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.

Ireton, G.C., Black, M.E., Stoddard, B.L.

(2003) Structure 11: 961-972

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Cytosine deaminase (CD) catalyzes the deamination of cytosine and is only present in prokaryotes and fungi, where it is a member of the pyrimidine salvage pathway. The enzyme is of interest both for antimicrobial drug design and gene therapy applicat ...

    Cytosine deaminase (CD) catalyzes the deamination of cytosine and is only present in prokaryotes and fungi, where it is a member of the pyrimidine salvage pathway. The enzyme is of interest both for antimicrobial drug design and gene therapy applications against tumors. The structure of Saccharomyces cerevisiae CD has been determined in the presence and absence of a mechanism-based inhibitor, at 1.14 and 1.43 A resolution, respectively. The enzyme forms an alpha/beta fold similar to bacterial cytidine deaminase, but with no similarity to the alpha/beta barrel fold used by bacterial cytosine deaminase or mammalian adenosine deaminase. The structures observed for bacterial, fungal, and mammalian nucleic acid deaminases represent an example of the parallel evolution of two unique protein folds to carry out the same reaction on a diverse array of substrates.

    Organizational Affiliation: 

    Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Avenue North A3-023, Seattle, WA 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytosine deaminase
A, B
161Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: FCY1
EC: 3.5.4.1
Find proteins for Q12178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12178
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HPY
Query on HPY
Download SDF File 
Download CCD File 
A, B
4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE
C4 H6 N2 O2
DEAAWXYGBWCVJW-VKHMYHEASA-N
 Ligand Interaction
ACY
Query on ACY
Download SDF File 
Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.110 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.880α = 90.00
b = 70.417β = 90.00
c = 71.523γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
CNSphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-19
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance