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Nucleic Acids Research Advance Access published online on December 14, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl1074
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acid Enzymes

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins

Veronika Németh-Pongrácz, Orsolya Barabás, Mónika Fuxreiter, István Simon, Iva Pichová1, Michalea Rumlová1, Helena Zábranská1, Dmitri Svergun2, Maxim Petoukhov2, Veronika Harmat3, Éva Klement4, Éva Hunyadi-Gulyás4, Katalin F. Medzihradszky4, Emese Kónya and Beáta G. Vértessy*

Institute of Enzymology, BRC, Hungarian Academy of Sciences Budapest, Karolina út 29, H-1113, Hungary 1 Institute of Chemistry and Biochemistry, Czech Academy of Sciences Prague, Czech Republic 2 European Molecular Biology Laboratory, Hamburg Outstation Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia 3 Hungarian Academy of Sciences-Eotvos Lorand University, Protein Modeling Research Group Budapest, Hungary 4 Proteomics Laboratory, Biological Research Center Hungarian Academy of Sciences, Szeged, Hungary

*To whom correspondence should be addressed. Tel: 36 12793116; Fax: 36 14665465; Email: vertessy{at}enzim.hu

Received September 8, 2006. Revised November 8, 2006. Accepted November 10, 2006.

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 ß-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.


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