Structure of the RNA polymerase domain of E. coli primase

Science

Volumn 287, Issue 5462, 2000, Pages 2482-2486

  Keck, James L ^a   Roche, Daniel D ^b   Lynch, A Simon ^b   Berger, James M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b AMGEN INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA PRIMASE; RNA POLYMERASE; SINGLE STRANDED DNA;

ARTICLE; DNA REPLICATION; DNA STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DNA HELICASES; DNA PRIMASE; DNA REPLICATION; DNA, BACTERIAL; DNA, SINGLE-STRANDED; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; METALS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; RNA; TEMPLATES, GENETIC;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0034737468     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.287.5462.2482     Document Type: Article

References (44)

1. D. Brutlag, R. Schekman, A. Kornberg, Proc. Natl. Acad. Sci. U.S.A. 68, 2826 (1971).
2. A. Kornberg and T. A. Baker, DNA Replication (Freeman, New York, ed. 2, 1992).
3. E. L. Zechner, C. A. Wu, K. J. Marians, J. Biol. Chem. 267, 4054 (1992).
4. K. Tougu and K. J. Marians, J. Biol. Chem. 271, 21398 (1996).
5. Y. B. Lu, P. V. Ratnakar, B. K. Mohanty, D. Bastia, Proc. Natl. Acad. Sci. U.S.A. 93, 12902 (1996).
6. A. Yuzhakov, Z. Kelman, M. O'Donnell, Cell 96, 153 (1999).
7. T. Kitani, K. Yoda, T. Ogawa, T. Okazaki, J. Mol. Biol. 184, 45 (1985).
8. K. J. Marians, Annu. Rev. Biochem. 61, 673 (1992).
9. K. Tougu, H. Peng, K. J. Marians, J. Biol. Chem. 269, 4675 (1994).
10. W. Sun, J. Tormo, T. A. Steitz, G. N. Godson, Proc. Natl. Acad. Sci. U.S.A. 91, 11462 (1994).
11. J. L. Keck, D. D. Roche, A. S. Lynch, J. M. Berger, data not shown.
12. 1 with unit cell lengths a = 39, b = 58, c = 149 Å were formed.
13. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
14. free of 27.6% by using Refmac/ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
15. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
16. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
17. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
18. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
19. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
20. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
21. free of 27.6% by using Refmac/ ARP [G. N. Murshudov, A. A. Vagin, E. J. Dodson, Acta Cystallogr. D 53, 240 (1997); V. S. Lamzin and K. S. Wilson, Acta Cystallogr. D 49, 129 (1993)]. The final model includes residues 115 to 428, with the exception of residues 192 to 194 and 287, for which electron density was not observed. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
22. α atoms between the two structures is 0.6 Å. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
23. α atoms between the two structures is 0.6 Å. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
24. α atoms between the two structures is 0.6 Å. No bond angles for this model fall into either disallowed or generously allowed regions of Ramachandrian space.
25. L. Holm and C. Sander, J. Mol. Biol. 233, 123 (1993).
26. L. Aravind, D. D. Leipe, E. V. Koonin, Nucleic Acids Res. 26, 4205 (1998).
27. J. M. Berger, D. Fass, J. C. Wang, S. C. Harrison, Proc. Natl. Acad. Sci. U.S.A. 95, 7876 (1998).
28. J. Versalovic and J. R. Lupski, Gene 136, 281 (1993).
29. T. V. Ilyina, A. E. Gorbalenya, E. V. Koonin, J. Mol. Evol. 34, 351 (1992).
30. G. Ziegelin, N. A. Linderoth, R. Calendar, E. Lanka, J. Bacteriol. 177, 4333 (1995).
31. W. Sun, J. Schoneich, G. N. Godson, J. Bacteriol. 181, 3761 (1999).
32. M. D. Nichols, K. DeAngelis, J. L. Keck, J. M. Berger, EMBO J. 18, 6177 (1999).
33. T. A. Steitz, J. Biol. Chem. 274, 17395 (1999).
34. H. H. Egelman, X. Yu, R. Wild, M. M. Hingorani, S. S. Patel, Proc. Natl. Acad. Sci. U.S.A. 92, 3869 (1995).
35. X. Yu, M. M. Hingorani, S. S. Patel, E. H. Egelman, Nature Struct. Biol. 3, 740 (1996).
36. T. Kusakabe, K. Baradaran, J. Lee, C. C. Richardson, EMBO J. 17, 1542 (1998).
37. M. Carson, J. Appl. Crystallogr. 24, 958 (1991).
38. J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, D. G. Higgins, Nucleic Acids Res. 25, 4876 (1997).
39. S. A. Benner, M. A. Cohen, G. H. Gonnet, Protein Eng. 7, 1323 (1994).
40. W. Kabsch and C. Sanders, Biopolymers 22, 2577 (1983).
41. A. Nicholls, K. A. Sharp, B. Honig, Proteins 11, 281 (1991).
42. D. L. Ollis, P. Brick, R. Hamlin, N. G. Xuong, T. A. Steitz, Nature 313, 762 (1985).
43. M. J. Jezewska, S. Rajendran, D. Bujalowska, W. Bujalowski, J. Biol. Chem. 273, 10515 (1998).
44. We thank the 5.0.2 beamline staff at the Advanced Light Source (Lawrence Berkeley National Laboratories) for assistance with measurements and J. Holton and O. Littlefield for helpful discussions. We also thank M. Botchan, R. Calendar, N. Cozzarelli, S. Gradia, R. Fennell-Fezzie, and K. DeAngelis for assistance with the manuscript and E. Egelman for providing electron micrograph reconstructions of the T7 primase-helicase. Supported by the G. Harold and Leila Y. Mathers Charitable Foundation (J.M.B.) and The Jane Coffin Childs Memorial Fund for Medical Research (J.L.K.). The crystallographic coordinates of both structures have been deposited in the RCSB Protein Data Bank (accession codes: 1DD9 and 1DDE).