1F7D

CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of feline immunodeficiency virus dUTP pyrophosphatase and its nucleotide complexes in three crystal forms.

Prasad, G.S.Stura, E.A.Elder, J.H.Stout, C.D.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1100-1109

  • DOI: 10.1107/s0907444900009197
  • Primary Citation of Related Structures:  
    1F7R, 1F7D, 1F7Q, 1F7P, 1F7O, 1F7N, 1F7K

  • PubMed Abstract: 
  • dUTP pyrophosphatase (dUTPase) cleaves the alpha-beta phosphodiester of dUTP to form pyrophosphate and dUMP, preventing incorporation of uracil into DNA and providing the substrate for thymine synthesis. Seven crystal structures of feline immunodefic ...

    dUTP pyrophosphatase (dUTPase) cleaves the alpha-beta phosphodiester of dUTP to form pyrophosphate and dUMP, preventing incorporation of uracil into DNA and providing the substrate for thymine synthesis. Seven crystal structures of feline immunodeficiency virus (FIV) dUTPase in three crystal forms have been determined, including complexes with substrate (dUTP), product (dUMP) or inhibitor (dUDP) bound. The native enzyme has been refined at 1.40 A resolution in a hexagonal crystal form and at 2.3 A resolution in an orthorhombic crystal form. In the dUDP complex in a cubic crystal form refined at 2.5 A resolution, the C-terminal conserved P-loop motif is fully ordered. The analysis defines the roles of five sequence motifs in interaction with uracil, deoxyribose and the alpha-, beta- and gamma-phosphates. The enzyme utilizes adaptive recognition to bind the alpha- and beta-phosphates. In particular, the alpha-beta phosphodiester adopts an unfavorable eclipsed conformation in the presence of the P-loop. This conformation may be relevant to the mechanism of alpha-beta phosphodiester bond cleavage.


    Related Citations: 
    • Crystal Structure of dUTP Pyrophosphatase from Feline Immunodeficiency Virus
      Prasad, G.S., Stura, E.A., McRee, D.E., Laco, G.S., Hasselkus-Light, C., Elder, J.H., Stout, C.D.
      (1996) Protein Sci 5: 2429

    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037-1093, USA. prasad@scripps.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POL POLYPROTEINAB136Feline immunodeficiency virusMutation(s): 0 
EC: 3.6.1.23 (PDB Primary Data), 3.4.23 (UniProt), 2.7.7.49 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P16088 (Feline immunodeficiency virus (isolate Petaluma))
Explore P16088 
Go to UniProtKB:  P16088
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.179 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.057α = 90
b = 77.057β = 90
c = 86.117γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description