Dpo4 is hindered in extending a G·T mismatch by a reverse wobble

Nature Structural and Molecular Biology

Volumn 11, Issue 5, 2004, Pages 457-462

  Trincao, Jose ^a   Johnson, Robert E ^b   Wolfle, William T ^b   Escalante, Carlos R ^a   Prakash, Satya ^b   Prakash, Louise ^b   Aggarwal, Aneel K ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DNA POLYMERASE; GUANINE; HYDROXYL GROUP; PRIMER DNA; PROTEIN; PROTEIN DPO4; THYMINE; UNCLASSIFIED DRUG;

ARTICLE; BASE MISPAIRING; BASE PAIRING; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA TEMPLATE; GENE MUTATION; GENOME; GEOMETRY; KINETICS; MOLECULAR DYNAMICS; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE;

BACTERIAL PROTEINS; BASE PAIR MISMATCH; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA PRIMERS; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; SULFOLOBUS;

SULFOLOBUS; SULFOLOBUS SOLFATARICUS;

EID: 2342644853     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb755     Document Type: Article

References (32)

1. Goodman, M.F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71, 17-50 (2002).
2. Prakash, S. & Prakash, L. Translesion DNA synthesis in eukaryotes: a one- or two-polymerase affair. Genes Dev. 16, 1872-1883 (2002).
3. Doublie, S., Sawaya, M.R. & Ellenberger, T. An open and closed case for all polymerases. Structure 7, R31-R35 (1999).
4. Mendelman, L.V., Petruska, J. & Goodman, M.F. Base mispair extension kinetics. Comparison of DNA polymerase α and reverse transcriptase. J. Biol. Chem. 265, 2338-2346 (1990).
5. Huang, M.-M., Arnheim, N. & Goodman, M.F. Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR. Nucleic Acids Res. 20, 4567-4573 (1992).
6. Joyce, C.M., Sun, X.C. & Grindley, N.D. Reactions at the polymerase active site that contribute to the fidelity of Escherichia coli DNA polymerase I (Klenow fragment). J. Biol. Chem. 267, 24485-24500 (1992).
7. Washington, M.T., Johnson, R.E., Prakash, S. & Prakash, L. Mismatch extension ability of yeast and human DNA polymerase η. J. Biol. Chem. 276, 2263-2266 (2001).
8. Vaisman, A., Tissier, A., Frank, E.G., Goodman, M.F. & Woodgate, R. Human DNA polymerase t promiscuous mismatch extension. J. Biol. Chem. 276, 30615-30622 (2001).
9. Washington, M.T., Johnson, R.E., Prakash, L. & Prakash, S. Human DINB1-encoded DNA polymerase κ is a promiscuous extender of mispaired primer termini. Proc. Nat. Acad. Sci. USA 99, 1910-1914 (2002).
10. Haracska, L., Prakash, L. & Prakash, S. Role of human DNA polymerase κ as an extender in translesion synthesis. Proc. Nat. Acad. Sci. USA 99, 16000-16005 (2002).
11. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107, 91-102 (2001).
12. Ling, H., Boudsocq, F., Plosky, B.S., Woodgate, R. & Yang, W. Replication of cis-syn thymine dimer at atomic resolution. Nature 242, 1083-1087 (2003).
13. Steitz, T.A. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274, 17395-17398 (1999).
14. Trincao, J. et al. Structure of the catalytic core of S. cerevisiae DNA polymerase η: implications for translesion DNA synthesis. Mol. Cell 8, 417-426 (2001).
15. Zhou, B.-L., Pata, J.D. & Steitz, T. A. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol. Cell 8, 427-437 (2001).
16. Silvian, L.F., Toth, E.A., Pham, P., Goodman, M.F. & Ellenberger, T. Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat. Struct. Biol. 8, 984-989 (2001).
17. Johnson, R.E., Trincao, J., Aggarwal, A.K., Prakash, S. & Prakash, L. Deoxynucleotide triphosphate binding mode conserved in Y family DNA polymerases. Mol. Cell. Biol. 23, 3008-3012 (2003).
18. Leontis, N.B., Stombaugh, J. & Westhof, E. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 30, 3497-3531 (2002).
19. Hunter, W.N., Kneale, G., Brown, T., Rabinovich, D. & Kennard, O. Refined crystal structure of an actanucleotide duplex with G·T mismatched base-pairs. J. Mol. Biol. 190, 605-618 (1986).
20. Hare, D., Shapiro, L. & Patel, D.J. Wobble dG × dT pairing in right-handed DNA: solution conformation of the d(C-G-T-G-A-A-T-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra. Biochemistry 25, 7445-7456 (1986).
21. Mooers, B.H., Eichman, B.F. & Ho, P.S. The structures and relative stabilities of d(G × G) reverse Hoogsteen, d(G × T) reverse wobble, and d(G × C) reverse Watson-Crick base-pairs in DNA crystals. J. Mol. Biol. 269, 796-810 (1997).
22. Perrino, F.W. & Loeb, L.A. Differential extension of 3′ mispairs is a major contribution to the high fidelity of calf thymus DNA polymerase α. J. Biol. Chem. 264, 2898-2905 (1989).
23. Varani, G., Cheong, C. & Tinoco, I. Jr. Structure of an unusually stable RNA hairpin. Biochemistry 30, 3280-3289 (1991).
24. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289, 905-920 (2000).
25. Bullock, T.L., Sherlin, L.D. & Perona, J.J. Tertiary core rearrangements in a tight binding transfer RNA aptamer. Nat. Struct. Biol. 7, 497-504 (2000).
26. Klinck, R. et al. A potential RNA drug target in the hepatitis C virus internal ribosomal entry site. RNA 6, 1423-1431 (2000).
27. Johnson, R.E., Yu, S.-L., Prakash, S. & Prakash, L. Yeast DNA polymerase zeta (ζ) is essential for error-free replication past thymine glycol. Genes Dev. 17, 77-87 (2003).
28. Johnson, R.E., Washington, M.T., Prakash, S. & Prakash, L. Fidelity of human DNA polymerase η. J. Biol. Chem. 275, 7447-7450 (2000).
29. Aggarwal, A.K. Crystallization of DNA binding proteins with oligodeoxynucleotides. Methods 1, 83-90 (1990).
30. Brunger, A.T. et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
31. Jones, A.T., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
32. Koradi, R., Billeter, M, & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55 (1996).