Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 44.19 kDa 
• Atom Count: 2832 
• Modelled Residue Count: 347 
• Deposited Residue Count: 408 
• Unique protein chains: 1

1F7O

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

• PDB DOI: 10.2210/pdb1F7O/pdb

• Classification: Viral protein, hydrolase
• Organism(s): Feline immunodeficiency virus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2000-06-27 Released: 2000-09-06 
• Deposition Author(s): Prasad, G.S., Stura, E.A., Elder, J.H., Stout, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.286 
• R-Value Observed: 0.216 

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

• PubMed: 10957629 
• DOI: 10.1107/s0907444900009197
• Primary Citation of Related Structures:  
  1F7D, 1F7K, 1F7N, 1F7O, 1F7P, 1F7Q, 1F7R


• 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 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.

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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

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037-1093, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POL POLYPROTEIN	A, B, C	136	Feline immunodeficiency virus	Mutation(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)
UniProt
Find proteins for P16088 (Feline immunodeficiency virus (isolate Petaluma)) Explore P16088  Go to UniProtKB:  P16088

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.286 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.29	α = 90
b = 71.7	β = 90
c = 77.04	γ = 90

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-06-27 
• Released Date: 2000-09-06 
Deposition Author(s): Prasad, G.S., Stura, E.A., Elder, J.H., Stout, C.D.

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: Version format compliance