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Structure and mechanism of human DNA polymerase η

Nature volume 465, pages 1044–1048 (2010)Cite this article

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A Corrigendum to this article was published on 03 August 2011

Abstract

The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase η (Polη), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Polη at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Polη acts like a ‘molecular splint’ to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Polη orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Polη missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Polη in replicating through D loop and DNA fragile sites.

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Figure 1: Structure of human Polη.
Figure 2: Structures of lesion DNAs.
Figure 3: Functional analyses of Q38A and R61A mutant Polη.
Figure 4: Human Polη is a molecular splint.
Figure 5: XPV mutations.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structures have been deposited with the Protein Data Bank under accession codes 3MR2 (Nrm), 3MR3 (TT1), 3MR4 (TT2), 3MR5 (TT3) and 3MR6 (TT4).

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Acknowledgements

We thank D. Leahy, M. Gellert and R. Craigie for critical reading of the manuscript. The research was funded by the intramural research program of NIDDK, NIH, and grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. Y.Z. is the recipient of a Chinese Ministry of Education scholarship and joint PhD student in NIH-Zhejiang University Graduate Partnership Program. S.R.-M. received a fellowship from the Human Frontiers Science Program.

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Author notes

  1. Santiago Ramón-Maiques & Jae Young Lee

    Present address: Present addresses: Spanish National Cancer Research Centre, Madrid 28029, Spain (S.R.-M.); Dongguk University-Seoul, Seoul 100-715, Korea (J.Y.L.).,

Authors and Affiliations

  1. Laboratory of Molecular Biology, NIDDK, NIH, 9000 Rockville Pike, Building 5, Room B103, Bethesda, Maryland 20892, USA,

    Christian Biertümpfel, Ye Zhao, Santiago Ramón-Maiques, Mark Gregory, Jae Young Lee & Wei Yang

  2. Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China

    Ye Zhao

  3. Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan

    Yuji Kondo, Chikahide Masutani & Fumio Hanaoka

  4. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK,

    Alan R. Lehmann

  5. Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan,

    Fumio Hanaoka

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Contributions

C.B. determined the five structures; Y.Z. prepared the samples and grew the crystals; Y.K. did the kinetic and bypass assays; S.R.-M. determined the type 1 structure; M.G. prepared the clone and type 1 crystals; J.Y.L. made mutants; C.M. designed the functional assays; A.R.L. identified the unpublished XPV mutations; F.H. conceived the project; and W.Y. supervised the structure determination. C.B., Y.Z., F.H. and W.Y. prepared the manuscript. C.B. and Y.Z. contributed equally to the study. All authors discussed the results and commented on the manuscript.

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Correspondence to Fumio Hanaoka or Wei Yang.

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Biertümpfel, C., Zhao, Y., Kondo, Y. et al. Structure and mechanism of human DNA polymerase η. Nature 465, 1044–1048 (2010). https://doi.org/10.1038/nature09196

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