1OX7 | pdb_00001ox7

Crystal structure of yeast cytosine deaminase apo-enzyme: inorganic zinc bound

• PDB DOI: https://doi.org/10.2210/pdb1OX7/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-04-01 Released: 2003-08-19 
• Deposition Author(s): Ireton, G.C., Black, M.E., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

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

• PubMed: 12906827 
• DOI: https://doi.org/10.1016/s0969-2126(03)00153-9
• Primary Citation Related Structures: 
  1OX7, 1P6O


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.48 kDa 
• Atom Count: 2,838 
• Modeled Residue Count: 319 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A, B	161	Saccharomyces cerevisiae	Mutation(s): 7  Gene Names: FCY1 OR YPR062W OR YP9499.17 EC: 3.5.4.1
UniProt
Find proteins for Q12178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12178  Go to UniProtKB:  Q12178

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.491	α = 90
b = 70.467	β = 90
c = 71.941	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-19 
Deposition Author(s): Ireton, G.C., Black, M.E., Stoddard, B.L.

Revision History  

• Version 1.0: 2003-08-19
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary