Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 359, Issue 1441, 2004, Pages 17-23

  Steitz, Thomas A ^a,b   Yin, Y Whitney ^a  

^a YALE UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

DNA polymerase; Protein structure; Replication; RNA polymerase; Translocation

Indexed keywords

DNA; RNA;

EID: 1642524959     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2003.1374     Document Type: Conference Paper

References (41)

1. Bedford, E., Tabor, S. & Richardson, C. C. 1997 The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I. Proc. Natl Acad. Sci. USA 94, 479-484.
2. Beese, L. S. & Steitz, T. A. 1991 Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J. 10, 25-33.
3. Beese, L. S., Derbyshire, V. & Steitz, T. A. 1993a Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260, 352-355.
4. Beese, L. S., Friedman, J. M. & Steitz, T. A. 1993b Crystal structure of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. Biochem. 32, 14 095-14 101.
5. Bernad, A., Blanco, L. & Salas, M. 1990 Site-directed mutagenesis of the YCDTDS amino acid motif of the phi 29 DNA polymerase. Gene 94, 45-51.
6. Brautigam, C. A. & Steitz, T. A. 1998 Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 8, 54-63.
7. Cheetham, G. M. & Steitz, T. A. 1999 Structure of a transcribing TV RNA polymerase initiation complex. Science 286, 2305-2309.
8. Cheetham, G. M., Jeruzalmi, D. & Steitz, T. A. 1998 Transcription regulation, initiation, and 'DNA scrunching' by T7 RNA polymerase. Cold Spring Harbor Symp. Quant. Biol. 63, 263-267.
9. Doublié, S., Tabor, S., Long, A. M., Richardson, C. C. & Ellenberger, T. 1998 Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391, 251-258.
10. Doublié, S., Sawaya, M. R. & Ellenberger, T. 1999 An open and closed case for all polymerases. Structure Folding Design 7, R31-35.
11. Franklin, M. C., Wang, J. & Steitz, T. A. 2001 Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105, 657-667.
12. Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R. & Steitz, T. A. 1988 Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. Natl Acad. Sci. USA 85, 8924-8928.
13. Friedberg, E. C. & Gerlach, V. L. 1999 Novel DNA polymerases offer clues to the molecular basis of mutagenesis. Cell 98, 413-416.
14. Friedberg, E. C., Feaver, W. J. & Gerlach, V. L. 2000 The many faces of DNA polymerases: strategies for mutagenesis and for mutational avoidance. Proc. Natl Acad. Sci. USA 97, 5681-5683.
15. Goodman, M. F. & Tippin, B. 2000 The expanding polymerase universe. Nature Rev. Mol. Cell Biol. 1, 101-109.
16. Goodrich, L. D., Lin, T. C., Spicer, E. K., Jones, C. & Konigsberg, W. H. 1997 Residues at the carboxy terminus of T4 DNA polymerase are important determinants for interaction with the polymerase accessory proteins. Biochem. 36, 10 474-10 481.
17. Huang, H., Chopra, R., Verdine, G. L. & Harrison, S. C. 1998 Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282, 1669-1675.
18. Johnson, R. E., Washington, M. T., Prakash, S. & Prakash, L. 1999 Bridging the gap: a family of novel DNA polymerases that replicate faulty DNA. Proc. Natl Acad. Sci. USA 96, 12 224-12 226.
19. Johnson, S. J., Taylor, J. S. & Beese, L. S. 2003 Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc. Natl Acad. Sci. USA 100, 3895-3900.
20. Kiefer, J. R., Mao, C., Braman, J. C. & Beese, L. S. 1998 Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391, 304-307.
21. Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A. & Steitz, T. A. 1992 Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256, 1783-1790.
22. Kornberg, A. & Baker, T. 1992 DNA replication, 2nd edn. New York: W. H. Freeman & Co.
23. Li, Y., Kong, Y., Korolev, S. & Waksman, G. 1998a Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. Protein Sci. 7, 1116-1123.
24. Li, Y., Korolev, S. & Waksman, G. 1998b Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J. 17, 7514-7525.
25. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. 2001 Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107, 91-102.
26. Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G. & Steitz, T. A. 1985a Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Nature 313, 762-766.
27. Ollis, D. L., Kline, C. & Steitz, T. A. 1985b Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Nature 313, 818-819.
28. Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H. & Kraut, J. 1994 Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science 264, 1891-1903.
29. Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H. & Kraut, J. 1996 Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. Biochem. 35, 12 742-12 761.
30. Sawaya, M. R., Pelletier, H., Kumar, A., Wilson, S. H. & Kraut, J. 1994 Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science 264, 1930-1935.
31. Shamoo, Y. & Steitz, T. A. 1999 Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell 99, 155-166.
32. Shamoo, Y., Friedman, A. M., Parsons, M. R., Konigsberg, W. H. & Steitz, T. A. 1995 Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Nature 376, 362-366.
33. Steitz, T. A. 1999 DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274, 17 395-17 398.
34. Steitz, T. A. & Steitz, J. A. 1993 A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA 90, 6498-6502.
35. Steitz, T. A., Smerdon, S. J., Jager, J. & Joyce, C. M. 1994 A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science 266, 2022-2025.
36. Wang, J., Sattar, A. K., Wang, C. C., Karam, J. D., Konigsberg, W. H. & Steitz, T. A. 1997 Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69. Cell 89, 1087-1099.
37. Woodgate, R. 1999 A plethora of lesion-replicating DNA polymerases. Genes Dev. 13, 2191-2195.
38. Yeh, L. S., Hsu, T. Y. & Karam, J. D. 1998 Divergence of a DNA replication gene cluster in the T4-related bacteriophage RB69. J. Bacteriol. 180, 2005-2013.
39. Yin, Y. W. & Steitz, T. A. 2002 Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298, 1387-1395.
40. Yin, Y. W. & Steitz, T. A. 2004 The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 116. (Submitted.)
41. Zhou, B. L., Pata, J. D. & Steitz, T. A. 2001 Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Mol. Cell 8, 427-437.