Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next?

Computational and Structural Biotechnology Journal

Volumn 13, Issue , 2015, Pages 339-351

  Boudet, Julien ^a   Devillier, Jean Christophe ^b   Allain, Frédéric H T ^a   Lipps, Georg ^b  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF APPLIED SCIENCES AND ARTS NORTHWESTERN SWITZERLAND   (Switzerland)

Author keywords

Catalysis; Dinucleotide formation; DNA template; High resolution structures; Primases; Primer synthesis

Indexed keywords

COMPLEMENT; DNA PRIMASE; IRON; SULFUR; ZINC;

ALPHA HELIX; BINDING AFFINITY; CATALYSIS; DNA TEMPLATE; ENZYMATIC ASSAY; ENZYME ACTIVE SITE; ENZYME MECHANISM; HYPERTHERMOPHILIC ARCHAEON; LIGAND BINDING; MATHEMATICAL MODEL; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; REVIEW;

EID: 84948772198     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.1016/j.csbj.2015.04.006     Document Type: Review

References (61)

1. E. Schwob Flexibility and governance in eukaryotic DNA replication Curr Opin Microbiol 7 2004 680 690
2. D.N. Frick, and C.C. Richardson DNA primases Annu Rev Biochem 70 2001 39 80
3. A.A. Bocquier, L. Liu, I.K. Cann, K. Komori, D. Kohda, and Y. Ishino Archaeal primase: bridging the gap between RNA and DNA polymerases Curr Biol 11 2001 452 456
4. L.M. Iyer, E.V. Koonin, D.D. Leipe, and L. Aravind Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members Nucleic Acids Res 33 2005 3875 3896
5. M.A. Griep Primase structure and function Indian J Biochem Biophys 32 1995 171 178
6. P. Forterre The origin of viruses and their possible roles in major evolutionary transitions Virus Res 117 2006 5 16
7. R.D. Kuchta, and G. Stengel Mechanism and evolution of DNA primases Biochim Biophys Acta Proteins Proteomics 1804 2010 1180 1189
8. B. Arezi, and R.D. Kuchta Eukaryotic DNA primase Trends Biochem Sci 25 2000 572 576
9. N. Ito, I. Matsui, and E. Matsui Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii FEBS J 274 2007 1340 1351
10. C. Maris, C. Dominguez, and F.H. Allain The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression FEBS J 272 2005 2118 2131
11. L. Aravind, D.D. Leipe, and E.V. Koonin Toprim - a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Nucleic Acids Res 26 1998 4205 4213
12. M.L. Kilkenny, M.A. Longo, R.L. Perera, and L. Pellegrini Structures of human primase reveal design of nucleotide elongation site and mode of Pol α tethering Proc Natl Acad Sci 110 2013 15961 15966
13. B.W. Kirk, and R.D. Kuchta Human DNA primase: anion inhibition, manganese stimulation, and their effects on in vitro start-site selection Biochemistry 38 1999 10126 10134
14. M. Suzuki, E. Savoysky, S. Izuta, M. Tatebe, T. Okajima, and S. Yoshida RNA priming coupled with DNA synthesis on natural template by calf thymus DNA polymerase alpha-primase Biochemistry 32 1993 12782 12792
15. M. O'Donnell, L. Langston, and B. Stillman Principles and concepts of DNA replication in bacteria, archaea, and eukarya Cold Spring Harb Perspect Biol 5 2013
16. K. Beck, and G. Lipps Properties of an unusual DNA primase from an archaeal plasmid Nucleic Acids Res 35 2007 5635 5645
17. S.H. Lao-Sirieix, and S.D. Bell The heterodimeric primase of the hyperthermophilic archaeon Sulfolobus solfataricus possesses DNA and RNA primase, polymerase and 3[prime]-terminal nucleotidyl transferase activities J Mol Biol 344 2004 1251 1263
18. R.J. Sheaff, and R.D. Kuchta Mechanism of calf thymus DNA primase: slow initiation, rapid polymerization, and intelligent termination Biochemistry 32 1993 3027 3037
19. B.W. Kirk, C. Harrington, F.W. Perrino, and R.D. Kuchta Eucaryotic DNA primase does not prefer to synthesize primers at pyrimidine rich DNA sequences when nucleoside triphosphates are present at concentrations found in whole cells Biochemistry 36 1997 6725 6731
20. M.A. Augustin, R. Huber, and J.T. Kaiser Crystal structure of a DNA-dependent RNA polymerase (DNA primase) Nat Struct Biol 8 2001 57 61
21. N. Ito, O. Nureki, M. Shirouzu, S. Yokoyama, and F. Hanaoka Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis Genes Cells 8 2003 913 923
22. S.-H. Lao-Sirieix, R.K. Nookala, P. Roversi, S.D. Bell, and L. Pellegrini Structure of the heterodimeric core primase Nat Struct Mol Biol 12 2005 1137 1144
23. G. Lipps, A.O. Weinzierl, G. von Scheven, C. Buchen, and P. Cramer Structure of a bifunctional DNA primase-polymerase Nat Struct Mol Biol 11 2004 157 162
24. R.L. Perera, R. Torella, S. Klinge, M.L. Kilkenny, J.D. Maman, and L. Pellegrini Mechanism for priming DNA synthesis by yeast DNA polymerase alpha Elife 2 2013 [e00482]
25. S. Vaithiyalingam, D.R. Arnett, A. Aggarwal, B.F. Eichman, E. Fanning, and W.J. Chazin Insights into eukaryotic primer synthesis from structures of the p48 subunit of human DNA primase J Mol Biol 426 2014 558 569
26. S. Geibel, S. Banchenko, M. Engel, E. Lanka, and W. Saenger Structure and function of primase RepB′ encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode Proc Natl Acad Sci 106 2009 7810 7815
27. +-ion catalysis and substrate specificity Mol Cell 22 2006 5 13
28. K. Beck, A. Vannini, P. Cramer, and G. Lipps The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis Nucleic Acids Res 38 2010 6707 6718
29. B. Arezi, B.W. Kirk, W.C. Copeland, and R.D. Kuchta Interactions of DNA with human DNA primase monitored with photoactivatable crosslinking agents: implications for the role of the p58 subunit Biochemistry 38 1999 12899 12907
30. W.C. Copeland, and X. Tan Active site mapping of the catalytic mouse primase subunit by alanine scanning mutagenesis J Biol Chem 270 1995 3905 3913
31. L.K. Zerbe, and R.D. Kuchta The p58 subunit of human DNA primase is important for primer initiation, elongation, and counting Biochemistry 41 2002 4891 4900
32. B.E. Weiner, H. Huang, B.M. Dattilo, M.J. Nilges, E. Fanning, and W.J. Chazin An iron-sulfur cluster in the C-terminal domain of the p58 Subunit of human DNA primase J Biol Chem 282 2007 33444 33451
33. S. Vaithiyalingam, E.M. Warren, B.F. Eichman, and W.J. Chazin Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase Proc Natl Acad Sci 107 2010 13684 13689
34. L. Sauguet, S. Klinge, R.L. Perera, J.D. Maman, and L. Pellegrini Shared active site architecture between the large subunit of eukaryotic primase and DNA photolyase PLoS One 5 2010 [e10083]
35. V.B. Agarkar, N.D. Babayeva, Y.I. Pavlov, and T.H. Tahirov Crystal structure of the C-terminal domain of human DNA primase large subunit Cell Cycle 10 2011 926 931
36. R.J. Sheaff, R.D. Kuchta, and D. Ilsley Calf thymus DNA polymerase alpha-primase: "communication" and primer-template movement between the two active sites Biochemistry 33 1994 2247 2254
37. H. Pelletier, M.R. Sawaya, A. Kumar, S.H. Wilson, and J. Kraut Structures of ternary complexes of rat DNA polymerase [beta], a DNA template-primer, and ddCTP Science 264 1994 1891 1903
38. K.E. Keller, N. Cavanaugh, and R.D. Kuchta Interaction of herpes primase with the sugar of a NTP Biochemistry 47 2008 8977 8984
39. Y. Huang, R. Baxter, B.S. Smith, C.L. Partch, C.L. Colbert, and J. Deisenhofer Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity Proc Natl Acad Sci U S A 103 2006 17701 17706
40. N.C Brissett, M.J. Martin, R.S. Pitcher, J. Bianchi, R. Juarez, A.J. Green, and et al. Structure of a preternary complex involving a prokaryotic NHEJ DNA polymerase Mol Cell 41 2011 221 231
41. P. Xie A model for dynamics of primer extension by eukaryotic DNA primase Eur Biophys J 40 2011 1157 1165
42. S. Cloutier, H. Hamel, M. Champagne, and W.V. Yotov Mapping of the human DNA primase 1 (PRIM1) to chromosome 12q13 Genomics 43 1997 398 401
43. W.V. Yotov, H. Hamel, G.E. Rivard, M.A. Champagne, P.A. Russo, J.M. Leclerc, and et al. Amplifications of DNA primase 1 (PRIM1) in human osteosarcoma Genes Chromosomes Cancer 26 1999 62 69
44. Z.M. Li, Z.C. Liu, Z.Z. Guan, X.F. Zhu, J.M. Zhou, B.F. Xie, and et al. Inhibition of DNA primase and induction of apoptosis by 3,3′-diethyl-9-methylthia-carbocyanine iodide in hepatocellular carcinoma BEL-7402 cells World J Gastroenterol 10 2004 514 520
45. E. Galanis, J. Buckner, D. Kimmel, R. Jenkins, B. Alderete, J. O'Fallon, and et al. Gene amplification as a prognostic factor in primary and secondary high-grade malignant gliomas Int J Oncol 13 1998 717 724
46. A. Wald, L. Corey, B. Timmler, A. Margaret, T. Warren, S. Tyring, and et al. Helicase-primase inhibitor pritelivir for HSV-2 infection N Engl J Med 370 2014 201 210
47. K. Chono, K. Katsumata, T. Kontani, M. Kobayashi, K. Sudo, T. Yokota, and et al. ASP2151, a novel helicase-primase inhibitor, possesses antiviral activity against varicella-zoster virus and herpes simplex virus types 1 and 2 J Antimicrob Chemother 65 2010 1733 1741
48. T. Biswas, K.D. Green, S. Garneau-Tsodikova, and O.V. Tsodikov Discovery of inhibitors of Bacillus anthracis primase DnaG Biochemistry 52 2013 6905 6910
49. G. Sanyal, and P. Doig Bacterial DNA replication enzymes as targets for antibacterial drug discovery Expert Opin Drug Discovery 7 2012 327 339
50. R.D. Kuchta, and L. Willhelm Inhibition of DNA primase by 9-beta-D-arabinofuranosyladenosine triphosphate Biochemistry 30 1991 797 803
51. W.B. Parker, and Y.C. Cheng Inhibition of DNA primase by nucleoside triphosphates and their arabinofuranosyl analogs Mol Pharmacol 31 1987 146 151
52. C.V. Catapano, K.B. Chandler, and D.J. Fernandes Inhibition of primer RNA formation in CCRF-CEM leukemia cells by fludarabine triphosphate Cancer Res 51 1991 1829 1835
53. C.V. Catapano, F.W. Perrino, and D.J. Fernandes Primer RNA chain termination induced by 9-beta-D-arabinofuranosyl-2-fluoroadenine 5′-triphosphate. A mechanism of DNA synthesis inhibition J Biol Chem 268 1993 7179 7185
54. K. Tamiya-Koizumi, T. Murate, M. Suzuki, C.M. Simbulan, M. Nakagawa, M. Takemura, and et al. Inhibition of DNA primase by sphingosine and its analogues parallels with their growth suppression of cultured human leukemic cells Biochem Mol Biol Int 41 1997 1179 1189
55. C.A. Stein Suramin: a novel antineoplastic agent with multiple potential mechanisms of action Cancer Res 53 1993 2239 2248
56. C.M. Simbulan, K. Tamiya-Koizumi, M. Suzuki, M. Shoji, T. Taki, and S. Yoshida Sphingosine inhibits the synthesis of RNA primers by primase in vitro Biochemistry 33 1994 9007 9012
57. Y. Ito, K. Tamiya-Koizumi, Y. Koide, M. Nakagawa, T. Kawade, A. Nishida, and et al. Structural requirements of sphingosine molecules for inhibition of DNA primase: biochemical and computational analyses Biochemistry 40 2001 11571 11577
58. A. Robinson, R.J. Causer, and N.E. Dixon Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target Curr Drug Targets 13 2012 352 372
59. M. Brooks, and L.B. Dumas DNA primase isolated from the yeast DNA primase-DNA polymerase complex. Immunoaffinity purification and analysis of RNA primer synthesis J Biol Chem 264 1989 3602 3610
60. A.G. Baranovskiy, Y. Zhang, Y. Suwa, N.D. Babayeva, J. Gu, Y.I. Pavlov, and et al. Crystal structure of the human primase J Biol Chem 290 2015 5635 5646
61. R. Pokorny, T. Klar, U. Hennecke, T. Carell, A. Batschauer, and L.O. Essen Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome Proc Natl Acad Sci U S A 105 2008 21023 21027