Human DNA polymerase η is pre-aligned for dNTP binding and catalysis

Journal of Molecular Biology

Volumn 415, Issue 4, 2012, Pages 627-634

  Ummat, Ajay ^a   Silverstein, Timothy D ^a   Jain, Rinku ^a   Buku, Angeliki ^a   Johnson, Robert E ^b   Prakash, Louise ^b   Prakash, Satya ^b   Aggarwal, Aneel K ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b University of Texas Medical Branch School of Medicine   (United States)

Author keywords

binding and catalysis; DNA polymerase; DNA repair; translesion DNA synthesis; Y family DNA polymerase

Indexed keywords

DEOXYRIBONUCLEOSIDE TRIPHOSPHATE; DNA DIRECTED DNA POLYMERASE ETA;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA BINDING; DNA CONFORMATION; DNA REPAIR; DNA REPLICATION; DNA SYNTHESIS; ENZYME ACTIVE SITE; ENZYME BINDING; ESCHERICHIA COLI; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION;

EID: 84856217776     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.11.038     Document Type: Article

References (34)

1. Doublie S., Sawaya M.R., and Ellenberger T. An open and closed case for all polymerases Structure 7 1999 R31 R35
2. Joyce C.M., and Benkovic S.J. DNA polymerase fidelity: kinetics, structure, and checkpoints Biochemistry 43 2004 14317 14324 (Pubitemid 39491965)
3. Rothwell P.J., and Waksman G. Structure and mechanism of DNA polymerases Adv. Protein Chem. 71 2005 401 440 (Pubitemid 41446935)
4. Prakash S., Johnson R.E., and Prakash L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function Annu. Rev. Biochem. 74 2005 317 353 (Pubitemid 40995510)
5. Washington M.T., Carlson K.D., Freudenthal B.D., and Pryor J.M. Variations on a theme: eukaryotic Y-family DNA polymerases Biochim. Biophys. Acta 1804 2010 1113 1123
6. Johnson R.E., Prakash S., and Prakash L. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Poleta Science 283 1999 1001 1004
7. Yoon J.H., Prakash L., and Prakash S. Highly error-free role of DNA polymerase eta in the replicative bypass of UV-induced pyrimidine dimers in mouse and human cells Proc. Natl Acad. Sci. USA 106 2009 18219 18224
8. Johnson R.E., Kondratick C.M., Prakash S., and Prakash L. hRAD30 mutations in the variant form of xeroderma pigmentosum [see comments] Science 285 1999 263 265 (Pubitemid 29330001)
9. Masutani C., Kusumoto R., Yamada A., Dohmae N., Yokoi M., and Yuasa M. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta [see comments] Nature 399 1999 700 704 (Pubitemid 29289067)
10. Inui H., Oh K.S., Nadem C., Ueda T., Khan S.G., and Metin A. Xeroderma pigmentosum-variant patients from America, Europe, and Asia J. Invest. Dermatol. 128 2008 2055 2068 (Pubitemid 352001227)
11. Washington M.T., Prakash L., and Prakash S. Yeast DNA polymerase eta utilizes an induced-fit mechanism of nucleotide incorporation Cell 107 2001 917 927 (Pubitemid 34084982)
12. Trincao J., Johnson R.E., Escalante C.R., Prakash S., Prakash L., and Aggarwal A.K. Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis Mol. Cell 8 2001 417 426 (Pubitemid 32831558)
13. Biertumpfel C., Zhao Y., Kondo Y., Ramon-Maiques S., Gregory M., and Lee J.Y. Structure and mechanism of human DNA polymerase eta Nature 465 2010 1044 1048
14. Silverstein T.D., Johnson R.E., Jain R., Prakash L., Prakash S., and Aggarwal A.K. Structural basis for the suppression of skin cancers by DNA polymerase eta Nature 465 2010 1039 1043
15. Alt A., Lammens K., Chiocchini C., Lammens A., Pieck J.C., and Kuch D. Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta Science 318 2007 967 970 (Pubitemid 350098991)
16. Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., and Wang X. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383
17. Steitz T.A. DNA polymerases: structural diversity and common mechanisms J. Biol. Chem. 274 1999 17395 17398
18. McCulloch S.D., and Kunkel T.A. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases Cell Res. 18 2008 148 161
19. Kim S.J., Beard W.A., Harvey J., Shock D.D., Knutson J.R., and Wilson S.H. Rapid segmental and subdomain motions of DNA polymerase beta J. Biol. Chem. 278 2003 5072 5081 (Pubitemid 36801017)
20. Purohit V., Grindley N.D., and Joyce C.M. Use of 2-aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment) Biochemistry 42 2003 10200 10211 (Pubitemid 37052040)
21. Rothwell P.J., Mitaksov V., and Waksman G. Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: implications for the molecular basis of fidelity in DNA polymerases Mol. Cell 19 2005 345 355 (Pubitemid 41074890)
22. Luo G., Wang M., Konigsberg W.H., and Xie X.S. Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase Proc. Natl Acad. Sci. USA 104 2007 12610 12615 (Pubitemid 47255202)
23. Santoso Y., Joyce C.M., Potapova O., Le Reste L., Hohlbein J., and Torella J.P. Conformational transitions in DNA polymerase I revealed by single-molecule FRET Proc. Natl Acad. Sci. USA 107 2010 715 720
24. Arndt J.W., Gong W., Zhong X., Showalter A.K., Liu J., and Dunlap C.A. Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes Biochemistry 40 2001 5368 5375 (Pubitemid 32458236)
25. Yang L., Arora K., Beard W.A., Wilson S.H., and Schlick T. Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly J. Am. Chem. Soc. 126 2004 8441 8453 (Pubitemid 38917967)
26. Joyce C.M., Potapova O., Delucia A.M., Huang X., Basu V.P., and Grindley N.D. Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity Biochemistry 47 2008 6103 6116 (Pubitemid 351812823)
27. Rechkoblit O., Malinina L., Cheng Y., Kuryavyi V., Broyde S., Geacintov N.E., and Patel D.J. Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion PLoS Biol. 4 2006 e11
28. Nair D.T., Johnson R.E., Prakash L., Prakash S., and Aggarwal A.K. An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site Structure 14 2006 749 755
29. Vaisman A., Ling H., Woodgate R., and Yang W. Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis EMBO J. 24 2005 2957 2967 (Pubitemid 41486333)
30. McCoy A.J., Grosse-Kunstleve R.W., Storoni L.C., and Read R.J. Likelihood-enhanced fast translation functions Acta Crystallogr., Sect. D: Biol. Crystallogr. 61 2005 458 464 (Pubitemid 43934606)
31. Adams P.D., Afonine P.V., Bunkoczi G., Chen V.B., Davis I.W., and Echols N. PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr., Sect. D: Biol. Crystallogr. 66 2010 213 221
32. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
33. Winn M.D., Murshudov G.N., and Papiz M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions Methods Enzymol. 374 2003 300 321 (Pubitemid 37531815)
34. Delano W.L. The PyMOL Molecular Graphics System 2002 Delano Scientific LLC San Carlos, CA