Structure of the heterodimeric core primase

Nature Structural and Molecular Biology

Volumn 12, Issue 12, 2005, Pages 1137-1144

  Lao Sirieix, Si Houy ^a   Nookala, Ravi K ^b   Roversi, Pietro ^c   Bell, Stephen D ^a   Pellegrini, Luca ^b  

^a HUTCHISON MRC RESEARCH CENTRE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA PRIMASE; PROTEIN SUBUNIT;

ARCHAEBACTERIUM; ARTICLE; CATALYSIS; CHEMICAL ANALYSIS; CRYSTALLOGRAPHY; DNA BINDING; EUKARYOTE; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; RNA SYNTHESIS; SITE DIRECTED MUTAGENESIS; SULFOLOBUS SOLFATARICUS;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BINDING SITES; CONSERVED SEQUENCE; DIMERIZATION; DNA PRIMASE; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SUBUNITS; SULFOLOBUS SOLFATARICUS;

ARCHAEA; EUKARYOTA; SULFOLOBUS SOLFATARICUS;

EID: 28544432330     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1013     Document Type: Article

References (39)

1. Kornberg, A. & Baker, T.A. DNA Replication 2nd edn (W.H. Freeman and Company, New York, 1992).
2. Frick, D.N. & Richardson, C.C. DNA primases. Annu. Rev. Biochem. 70, 39-80 (2001).
3. Iyer, L.M., Koonin, E.V., Leipe, D.D. & Aravind, L. Origin and evolution of the archaeoeukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res. 33, 3875-3896 (2005).
4. Foiani, M., Lucchini, G. & Plevani, P. The DNA polymerase α-primase complex couples DNA replication, cell-cycle progression and DNA-damage response. Trends Biochem. Sci. 22, 424-427 (1997).
5. Arezi, B. & Kuchta, R.D. Eukaryotic DNA primase. Trends Biochem. Sci. 25, 572-576 (2000).
6. Santocanale, C., Foiani, M., Lucchini, G. & Plevani, P. The isolated 48,000-dalton subunit of yeast DNA primase is sufficient for RNA primer synthesis. J. Biol. Chem. 268, 1343-1348 (1993).
7. Copeland, W.C. & Wang, T.S. Enzymatic characterization of the individual mammalian primase subunits reveals a biphasic mechanism for initiation of DNA replication. J. Biol. Chem. 268, 26179-26189 (1993).
8. Schneider, A. et al. Primase activity of human DNA polymerase α-primase. Divalent cations stabilize the enzyme activity of the p48 subunit. J. Biol. Chem. 273, 21608-21615 (1998).
9. Foiani, M., Santocanale, C., Plevani, P. & Lucchini, G. A single essential gene, PRI2, encodes the large subunit of DNA primase in Saccharomyces cerevisiae. Mol. Cell. Biol. 9, 3081-3087 (1989).
10. Arezi, B., Kirk, B.W., Copeland, W.C. & Kuchta, R.D. Interactions of DNA with human DNA primase monitored with photoactivatable crosslinking agents: implications for the role of the p58 subunit. Biochemistry 38, 12899-12907 (1999).
11. Zerbe, L.K. & Kuchta, R.D. The p58 subunit of human DNA primase is important for primer initiation, elongation, and counting. Biochemistry 41, 4891-4900 (2002).
12. Edgell, D.R. & Doolittle, W.F. Archaea and the origin(s) of DNA replication proteins. Cell 89, 995-998 (1997).
13. Dionne, I. et al. DNA replication in the hyperthermophilic archaeon Sulfolobus solfataricus. Biochem. Soc. Trans. 31, 674-676 (2003).
14. Grabowski, B. & Kelman, Z. Archeal DNA replication: eukaryal proteins in a bacterial context. Annu. Rev. Microbiol. 57, 487-516 (2003).
15. Desogus, G., Onesti, S., Brick, P., Rossi, M. & Pisani, F.M. Identification and characterization of a DNA primase from the hyperthermophilic archaeon Methanococcus jannaschii. Nucleic Acids Res. 27, 4444-4450 (1999).
16. Makarova, K.S. et al. Comparative genomics of the archaea (euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9, 608-628 (1999).
17. Bocquier, A.A. et al. Archaeal primase: bridging the gap between RNA and DNA polymerases. Curr. Biol. 11, 452-456 (2001).
18. Liu, L. et al. The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus. J. Biol. Chem. 276, 45484-45490 (2001).
19. Lao-Sirieix, S.H. & Bell, S.D. The heterodimeric primase of the hyperthermophilic archaeon Sulfolobus solfataricus possesses DNA and RNA primase, polymerase and 3′-terminal nucleotidyl transferase activities. J. Mol. Biol. 344, 1251-1263 (2004).
20. Augustin, M.A., Huber, R. & Kaiser, J.T. Crystal structure of a DNA-dependent RNA polymerase (DNA primase). Nat. Struct. Biol. 8, 57-61 (2001).
21. Ito, N., Nureki, O., Shirouzu, M., Yokoyama, S. & Hanaoka, F. Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells 8, 913-923 (2003).
22. Steitz, T.A., Smerdon, S.J., Jager, J. & Joyce, C.M. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science 266, 2022-2025 (1994).
23. Lipps, G., Weinzierl, A.O., von Scheven, G., Buchen, C. & Cramer, P. Structure of a bifunctional DNA primase-polymerase. Nat. Struct. Mol. Biol. 11, 157-162 (2004).
24. Marini, F. et al. A role for DNA primase in coupling DNA replication to DNA damage response. EMBO J. 16, 639-650 (1997).
25. Copeland, W.C. & Tan, X. Active site mapping of the catalytic mouse primase subunit by alanine scanning mutagenesis. J. Biol. Chem. 270, 3905-3913 (1995).
26. Holm, L. & Sander, C. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20, 478-480 (1995).
27. Matsui, E. et al. Distinct domain functions regulating de novo DNA synthesis of thermostable DNA primase from hyperthermophile Pyrococcus horikoshii. Biochemistry 42, 14968-14976 (2003).
28. Glaser, F. et al. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19, 163-164 (2003).
29. Pan, H. & Wigley, D.B. Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase. Structure Fold. Des. 8, 231-239 (2000).
30. Kato, M., Ito, T., Wagner, G. & Ellenberger, T. A molecular handoff between bacteriophage T7 DNA primase and T7 DNA polymerase initiates DNA synthesis. J. Biol. Chem. 279, 30554-30562 (2004).
31. Lu, X.J. & Olson, W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31, 5108-5121 (2003).
32. Norton, N.C.& Finzel, B.C. The structure of an RNA/DNA hybrid: a substrate of the ribonuclease activity of HIV-1 reverse transcriptase. J. Mol. Biol. 264, 521-533 (1996).
33. Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. & Kraut, J. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 264, 1891-1903 (1994).
34. Sheaff, R.J. & Kuchta, R.D. Mechanism of calf thymus DNA primase: slow initiation, rapid polymerization, and intelligent termination. Biochemistry 32, 3027-3037 (1993).
35. Weeks, C.M. & Miller, R. The design and implementation of SnB version 2.0. J. Appl. Crystallogr. 32, 120-124 (1999).
36. La Fortelle, E.D. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494 (1997).
37. Emsley, P. & Cowtan, K. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
38. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
39. Blanc, E., Roversi, P., Vonrhein, C., Flensburg, S.M. & Bricogne, G. Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Crystallogr. D 60, 2210-2221 (2004).