Structural basis for DNA duplex separation by a superfamily-2 helicase

Nature Structural and Molecular Biology

Volumn 14, Issue 7, 2007, Pages 647-652

  Büttner, Katharina ^a   Nehring, Sebastian ^a   Hopfner, Karl Peter ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA POLYMERASE; DOUBLE STRANDED DNA; HELICASE; RNA;

ARTICLE; COMPARATIVE STUDY; CRYSTAL STRUCTURE; DNA STRUCTURE; HEPATITIS C VIRUS; PRIORITY JOURNAL; STRUCTURE ANALYSIS; TRANSPORT KINETICS;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; ARCHAEOGLOBUS FULGIDUS; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; DNA HELICASES; HELIX-LOOP-HELIX MOTIFS; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION;

ARCHAEA; HEPATITIS C VIRUS;

EID: 34447132375     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1246     Document Type: Article

References (35)

1. Linder, P. & Kowalczykowski, S. Helicases and NTP-driven nucleic acid machines: structure, function and roles in human disease. Nucleic Acids Res. 34, 4081 (2006).
2. Houseley, J., LaCava, J. & Tollervey, D. RNA-quality control by the exosome. Nat. Rev. Mol. Cell Biol. 7, 529-539 (2006).
3. Frick, D.N. Step-by-step progress toward understanding the hepatitis C virus RNA helicase. Hepatology 43, 1392-1395 (2006).
4. Gorbalenya, A.E., Koonin, E.V., Donchenko, A.P. & Blinov, V.M. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17, 4713-4730 (1989).
5. Velankar, S.S., Soultanas, P., Dillingham, M.S., Subramanya, H.S. & Wigley, D.B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75-84 (1999).
6. Korolev, S., Hsieh, J., Gauss, G.H., Lohman, T.M. & Waksman, G. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90, 635-647 (1997).
7. Lee, J.Y., Yang, W. & Uvr, D. Helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell 127, 1349-1360 (2006).
8. Fischer, C.J., Maluf, N.K. & Lohman, T.M. Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA. J. Mol. Biol. 344, 1287-1309 (2004).
9. Bennett, R.J. & Keck, J.L. Structure and function of RecQ DNA helicases. Crit. Rev. Biochem. Mol. Biol. 39, 79-97 (2004).
10. Seki, M., Marini, F. & Wood, R.D. POLQ (Pol theta), a DNA polymerase and DNA-dependent ATPase in human cells. Nucleic Acids Res. 31, 6117-6126 (2003).
11. Oshige, M., Aoyagi, N., Harris, P.V., Burtis, K.C. & Sakaguchi, K. A new DNA polymerase species from Drosophila melanogaster: a probable mus308 gene product. Mutat. Res. 433, 183-192 (1999).
12. Dumont, S. et al. RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature 439, 105-108 (2006).
13. Levin, M.K., Gurjar, M. & Patel, S.S. A Brownian motor mechanism of translocation and strand separation by hepatitis C virus helicase. Nat. Struct. Mol. Biol. 12, 429-435 (2005).
14. Serebrov, V. & Pyle, A.M. Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase. Nature 430, 476-480 (2004).
15. Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S. & Yokoyama, S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125, 287-300 (2006).
16. Singleton, M.R., Scaife, S. & Wigley, D.B. Structural analysis of DNA replication fork reversal by RecG. Cell 107, 79-89 (2001).
17. Durr, H., Korner, C., Muller, M., Hickmann, V. & Hopfner, K.P. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121, 363-373 (2005).
18. Marini, F. & Wood, R.D. A human DNA helicase homologous to the DNA cross-link sensitivity protein Mus308. J. Biol. Chem. 277, 8716-8723 (2002).
19. McCaffrey, R., St Johnston, D. & Gonzalez-Reyes, A. Drosophila mus301/spindle-C encodes a helicase with an essential role in double-strand DNA break repair and meiotic progression. Genetics 174, 1273-1285 (2006).
20. Yoshimura, M. et al. Vertebrate POLQ and POLbeta cooperate in base excision repair of oxidative DNA damage. Mol. Cell 24, 115-125 (2006).
21. Koonin, E.V., Wolf, Y.I. & Aravind, L. Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res. 11, 240-252 (2001).
22. Guy, C.P. & Bolt, E.L. Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands. Nucleic Acids Res. 33, 3678-3690 (2005).
23. Fujikane, R., Komori, K., Shinagawa, H. & Ishino, Y. Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus. J. Biol. Chem. 280, 12351-12358 (2005).
24. Singleton, M.R., Dillingham, M.S., Gaudier, M., Kowalczykowski, S.C. & Wigley, D.B. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature 432, 187-193 (2004).
25. Bono, F., Ebert, J., Lorentzen, E. & Conti, E. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 126, 713-725 (2006).
26. Andersen, C.B. et al. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313, 1968-1972 (2006).
27. Kim, J.L. et al. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure 6, 89-100 (1998).
28. Levin, M.K., Gurjar, M.M. & Patel, S.S. ATP binding modulates the nucleic acid affinity of hepatitis C virus helicase. J. Biol. Chem. 278, 23311-23316 (2003).
29. Lam, A.M., Keeney, D. & Frick, D.N. Two novel conserved motifs in the hepatitis C virus NS3 protein critical for helicase action. J. Biol. Chem. 278, 44514-44524 (2003).
30. Jankowsky, E., Gross, C.H., Shuman, S. & Pyle, A.M. Active disruption of an RNA-protein interaction by a DExH/D RNA helicase. Science 291, 121-125 (2001).
31. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795-800 (1993).
32. Schneider, T.R. & Sheldrick, G.M. Substructure solution with SHELXD. Acta Crystallogr. D Biol. Crystallogr. 58, 1772-1779 (2002).
33. Turk, D. Weiterentwicklung eines programms fuer molekuelgraphik und elektrondichtemanipulation und seine anwendung auf verschiedene protein-strukturaufklaerungen. Thesis, Technical Univ. Munich, (1992).
34. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921 (1998).
35. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).