3C3I

Evolution of chlorella virus dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.

Homma, K.Moriyama, H.

(2009) Acta Crystallogr.,Sect.F 65: 1030-1034

  • DOI: 10.1107/S1744309109034459
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the p ...

    The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an amino-terminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P2(1)3 crystals with unit-cell parameter a = 106.65 A. In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but formed aggregates. Glycyl-seryl-tagged dUTPases yielded cubic P2(1)3 IL-3A crystals with unit-cell parameter a = 105.68 A and hexagonal P6(3) Mu-22 crystals with unit-cell parameters a = 132.07, c = 53.45 A, gamma = 120 degrees . Owing to the Thr84Arg mutation, Mu-22 dUTPase had different monomer-to-monomer interactions to those of IL-3A dUTPase.


    Related Citations: 
    • Chlorella virus-encoded deoxyuridine triphosphatases exhibit different temperature optima.
      Zhang, Y.,Moriyama, H.,Homma, K.,Van Etten, J.L.
      (2005) J.Virol. 79: 9945


    Organizational Affiliation

    Department of Chemistry, University of Nebraska-Lincoln, NE 68583-0304, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyuridine triphosphatase
A, B, C, D
141Paramecium bursaria Chlorella virus IL3AMutation(s): 2 
Find proteins for Q5I3E5 (Paramecium bursaria Chlorella virus IL3A)
Go to UniProtKB:  Q5I3E5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUD
Query on DUD

Download SDF File 
Download CCD File 
A, B
DEOXYURIDINE-5'-DIPHOSPHATE
C9 H14 N2 O11 P2
QHWZTVCCBMIIKE-SHYZEUOFSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 132.069α = 90.00
b = 132.069β = 90.00
c = 53.451γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
MOLREPphasing
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance