1YSD | pdb_00001ysd

Yeast Cytosine Deaminase Double Mutant

• PDB DOI: https://doi.org/10.2210/pdb1YSD/pdb

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


• Deposited: 2005-02-08 Released: 2005-05-17 
• Deposition Author(s): Korkegian, A., Black, M.E., Baker, D., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Computational thermostabilization of an enzyme.

Korkegian, A., Black, M.E., Baker, D., Stoddard, B.L.

(2005) Science 308: 857-860

• PubMed: 15879217 
• DOI: https://doi.org/10.1126/science.1107387
• Primary Citation Related Structures: 
  1YSB, 1YSD


• PubMed Abstract: 
  

  Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10 degrees C increase in apparent melting temperature T(m) and a 30-fold increase in half-life at 50 degrees C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.

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Organizational Affiliation: 
• Division of Basic Sciences, Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, 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: 35.91 kDa 
• Atom Count: 2,772 
• Modeled Residue Count: 317 
• 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): 2  Gene Names: FCY1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.35	α = 90
b = 54.77	β = 105.68
c = 68.4	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-17 
Deposition Author(s): Korkegian, A., Black, M.E., Baker, D., Stoddard, B.L.

Revision History  

• Version 1.0: 2005-05-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection