DNA polymerase η (Polη) is unique among eukaryotic polymerases in its proficient ability for error-free replication through ultraviolet-induced cyclobutane pyrimidine dimers, and inactivation of Polη (also known as POLH) in humans causes the variant form of xeroderma pigmentosum (XPV). We present the crystal structures of Saccharomyces cerevisiae Polη (also known as RAD30) in ternary complex with a cis-syn thymine-thymine (T-T) dimer and with undamaged DNA. The structures reveal that the ability of Polη to replicate efficiently through the ultraviolet-induced lesion derives from a simple and yet elegant mechanism, wherein the two Ts of the T-T dimer are accommodated in an active site cleft that is much more open than in other polymerases. We also show by structural, biochemical and genetic analysis that the two Ts are maintained in a stable configuration in the active site via interactions with Gln 55, Arg 73 and Met 74. Together, these features define the basis for Polη’s action on ultraviolet-damaged DNA that is crucial in suppressing the mutagenic and carcinogenic consequences of sun exposure, thereby reducing the incidence of skin cancers in humans.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
Nature Communications Open Access 19 October 2021
The active site residues Gln55 and Arg73 play a key role in DNA damage bypass by S. cerevisiae Pol η
Scientific Reports Open Access 09 July 2018
Comparative molecular dynamics studies of heterozygous open reading frames of DNA polymerase eta (η) in pathogenic yeast Candida albicans
Scientific Reports Open Access 25 January 2017
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Johnson, R. E., Kondratick, C. M., Prakash, S. & Prakash, L. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285, 263–265 (1999)
Masutani, C. et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399, 700–704 (1999)
Broughton, B. C. et al. Molecular analysis of mutations in DNA polymerase η in xeroderma pigmentosum-variant patients. Proc. Natl Acad. Sci. USA 99, 815–820 (2002)
Gratchev, A., Strein, P., Utikal, J. & Sergij, G. Molecular genetics of Xeroderma pigmentosum variant. Exp. Dermatol. 12, 529–536 (2003)
Inui, H. et al. Xeroderma pigmentosum-variant patients from America, Europe, and Asia. J. Invest. Dermatol. 128, 2055–2068 (2008)
Tanioka, M. et al. Molecular analysis of DNA polymerase eta gene in Japanese patients diagnosed as xeroderma pigmentosum variant type. J. Invest. Dermatol. 127, 1745–1751 (2007)
Johnson, R. E., Prakash, S. & Prakash, L. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Polη. Science 283, 1001–1004 (1999)
Prakash, S., Johnson, R. E. & Prakash, L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu. Rev. Biochem. 74, 317–353 (2005)
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)
Kondratick, C. M., Washington, M. T., Prakash, S. & Prakash, L. Acidic residues critical for the activity and biological function of yeast DNA polymerase η. Mol. Cell. Biol. 21, 2018–2025 (2001)
Doublié, S., Tabor, S., Long, A. M., Richardson, C. C. & Ellenberger, T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391, 251–258 (1998)
Li, Y., Korolev, S. & Waksman, G. 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 (1998)
Steitz, T. A. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274, 17395–17398 (1999)
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)
Nair, D. T., Johnson, R. E., Prakash, S., Prakash, L. & Aggarwal, A. K. Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing. Nature 430, 377–380 (2004)
Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S. & Aggarwal, A. K. Human DNA polymerase ι incorporates dCTP opposite template G via a G.C+ Hoogsteen base pair. Structure 13, 1569–1577 (2005)
Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S. & Aggarwal, A. K. Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science 309, 2219–2222 (2005)
Lone, S. et al. Human DNA polymerase κ encircles DNA: implications for mismatch extension and lesion bypass. Mol. Cell 25, 601–614 (2007)
Alt, A. et al. Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase η. Science 318, 967–970 (2007)
Rothwell, P. J. & Waksman, G. Structure and mechanism of DNA polymerases. Adv. Protein Chem. 71, 401–440 (2005)
Washington, M. T., Prakash, L. & Prakash, S. Yeast DNA polymerase η utilizes an induced-fit mechanism of nucleotide incorporation. Cell 107, 917–927 (2001)
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)
Vaisman, A., Ling, H., Woodgate, R. & Yang, W. Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. EMBO J. 24, 2957–2967 (2005)
Gietz, R. D. & Sugino, A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74, 527–534 (1988)
Johnson, R. E., Prakash, L. & Prakash, S. Yeast and human translesion DNA synthesis polymerases: expression, purification, and biochemical characterization. Methods Enzymol. 408, 390–407 (2006)
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)
McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D 61, 458–464 (2005)
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
Winn, M. D., Murshudov, G. N. & Papiz, M. Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300–321 (2003)
Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007)
Brünger, A. T. et al. Crystallography & NMR system: A software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)
We thank the staff at Brookhaven National Laboratory (beamlines X6A and X29) and the Advanced Photon Source (24ID) for facilitating X-ray data collection. We thank D. T. Nair, S. Lone, R. Vasquez-Del Carpio and M. Swan for discussions. This work was supported by NIH grants to A.K.A., S.P. and L.P.
The authors declare no competing financial interests.
About this article
Cite this article
Silverstein, T., Johnson, R., Jain, R. et al. Structural basis for the suppression of skin cancers by DNA polymerase η. Nature 465, 1039–1043 (2010). https://doi.org/10.1038/nature09104
Nature Communications (2021)
Nature Structural & Molecular Biology (2020)
Current Genetics (2020)
Cellular and Molecular Life Sciences (2020)
Current Genetics (2019)