2D4M

Crystal Structure of apo M-PMV dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.

Nemeth-Pongracz, V.Barabas, O.Fuxreiter, M.Simon, I.Pichova, I.Rumlova, M.Zabranska, H.Svergun, D.Petoukhov, M.Harmat, V.Klement, E.Hunyadi-Gulyas, E.Medzihradszky, K.F.Konya, E.Vertessy, B.G.

(2007) Nucleic Acids Res. 35: 495-505

  • DOI: 10.1093/nar/gkl1074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The homotrimeric fusion protein nucleocapsid (NC)-dUTPase combines domains that participate in RNA/DNA folding, reverse transcription, and DNA repair in Mason-Pfizer monkey betaretrovirus infected cells. The structural organization of the fusion prot ...

    The homotrimeric fusion protein nucleocapsid (NC)-dUTPase combines domains that participate in RNA/DNA folding, reverse transcription, and DNA repair in Mason-Pfizer monkey betaretrovirus infected cells. The structural organization of the fusion protein remained obscured by the N- and C-terminal flexible segments of dUTPase and the linker region connecting the two domains that are invisible in electron density maps. Small-angle X-ray scattering reveals that upon oligonucleotide binding the NC domains adopt the trimeric symmetry of dUTPase. High-resolution X-ray structures together with molecular modeling indicate that fusion with NC domains dramatically alters the conformation of the flexible C-terminus by perturbing the orientation of a critical beta-strand. Consequently, the C-terminal segment is capable of double backing upon the active site of its own monomer and stabilized by non-covalent interactions formed with the N-terminal segment. This co-folding of the dUTPase terminal segments, not observable in other homologous enzymes, is due to the presence of the fused NC domain. Structural and genomic advantages of fusing the NC domain to a shortened dUTPase in betaretroviruses and the possible physiological consequences are envisaged.


    Organizational Affiliation

    Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Karolina Ășt 29, H-1113, Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DU
A
152Mason-Pfizer monkey virusMutation(s): 1 
Gene Names: gag-pro
Find proteins for P07570 (Mason-Pfizer monkey virus)
Go to UniProtKB:  P07570
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 61.191α = 90.00
b = 61.191β = 90.00
c = 63.310γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-07-20
    Type: Database references
  • Version 1.4: 2017-10-11
    Type: Refinement description