Hostname: page-component-78c5997874-xbtfd Total loading time: 0 Render date: 2024-11-17T18:18:29.434Z Has data issue: false hasContentIssue false

Molecular mechanisms of xeroderma pigmentosum (XP) proteins

Published online by Cambridge University Press:  10 February 2016

Sandra C. Koch
Affiliation:
Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
Nina Simon
Affiliation:
Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
Charlotte Ebert
Affiliation:
Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
Thomas Carell*
Affiliation:
Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
*
*Authors for correspondence: Thomas Carell, Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr, 5-13, 81377 Munich, Germany. Tel.: +49 (0)89 2180 77755 Email: thomas.carell@cup.uni-muenchen.de

Abstract

Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA–XPG) are caused by mutations in genes involved in the NER process. The eighth gene, XPV, codes for the DNA polymerase ɳ, which replicates through DNA lesions in a process called translesion synthesis (TLS). Over the past decade, detailed structural information of these DNA repair proteins involved in eukaryotic NER and TLS have emerged. These structures allow us now to understand the molecular mechanism of the NER and TLS processes in quite some detail and we have begun to understand the broad substrate specificity of NER. In this review, we aim to highlight recent advances in the process of damage recognition and repair as well as damage tolerance by the XP proteins.

Type
Review
Copyright
Copyright © Cambridge University Press 2016 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abdulrahman, W., Iltis, I., Radu, L., Braun, C., Maglott-Roth, A., Giraudon, C., Egly, J. M. & Poterszman, A. (2013). ARCH domain of XPD, an anchoring platform for CAK that conditions TFIIH DNA repair and transcription activities. Proceedings of the National Academy of Sciences of the United States of America 110, E633E642.Google ScholarPubMed
Aboussekhra, A., Biggerstaff, M., Shivji, M. K., Vilpo, J. A., Moncollin, V., Podust, V. N., Protic, M., Hubscher, U., Egly, J. M. & Wood, R. D. (1995). Mammalian DNA nucleotide excision repair reconstituted with purified protein components. Cell 80, 859868.CrossRefGoogle ScholarPubMed
Alt, A., Lammens, K., Chiocchini, C., Lammens, A., Pieck, J. C., Kuch, D., Hopfner, K. P. & Carell, T. (2007). Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta. Science 318, 967970.Google Scholar
Araki, M., Masutani, C., Takemura, M., Uchida, A., Sugasawa, K., Kondoh, J., Ohkuma, Y. & Hanaoka, F. (2001). Centrosome protein centrin 2/caltractin 1 is part of the xeroderma pigmentosum group C complex that initiates global genome nucleotide excision repair. The Journal of Biological Chemistry 276, 1866518672.Google Scholar
Araujo, S. J., Nigg, E. A. & Wood, R. D. (2001). Strong functional interactions of TFIIH with XPC and XPG in human DNA nucleotide excision repair, without a preassembled repairosome. Molecular and Cellular Biology 21, 22812291.Google Scholar
Araujo, S. J., Tirode, F., Coin, F., Pospiech, H., Syvaoja, J. E., Stucki, M., Hubscher, U., Egly, J. M. & Wood, R. D. (2000). Nucleotide excision repair of DNA with recombinant human proteins: definition of the minimal set of factors, active forms of TFIIH, and modulation by CAK. Genes & Development 14, 349359.CrossRefGoogle ScholarPubMed
Asahina, H., Kuraoka, I., Shirakawa, M., Morita, E. H., Miura, N., Miyamoto, I., Ohtsuka, E., Okada, Y. & Tanaka, K. (1994). The XPA protein is a zinc metalloprotein with an ability to recognize various kinds of DNA damage. Nature Structural & Molecular Biology 315, 229237.Google Scholar
Batty, D., Rapic’-Otrin, V., Levine, A. S. & Wood, R. D. (2000a). Stable binding of human XPC complex to irradiated DNA confers strong discrimination for damaged sites. Journal of Molecular Biology 300, 275290.Google Scholar
Batty, D. P. & Wood, R. D. (2000b). Damage recognition in nucleotide excision repair of DNA. Gene 241, 193204.CrossRefGoogle ScholarPubMed
Bernardes de Jesus, B. M., Bjoras, M., Coin, F. & Egly, J. M. (2008). Dissection of the molecular defects caused by pathogenic mutations in the DNA repair factor XPC. Molecular and Cellular Biology 28, 72257235.Google Scholar
Berneburg, M. & Lehmann, A. R. (2001). Xeroderma pigmentosum and related disorders: defects in DNA repair and transcription. Advances in Genetics 43, 71102.Google Scholar
Biertumpfel, C., Zhao, Y., Kondo, Y., Ramon-Maiques, S., Gregory, M., Lee, J. Y., Masutani, C., Lehmann, A. R., Hanaoka, F. & Yang, W. (2010). Structure and mechanism of human DNA polymerase eta. Nature 465, 10441048.CrossRefGoogle ScholarPubMed
Bootsma, D. & Hoeijmakers, J. H. (1993). DNA repair. Engagement with transcription. Nature 363, 114115.Google Scholar
Bresson, A. & Fuchs, R. P. (2002). Lesion bypass in yeast cells: Pol eta participates in a multi-DNA polymerase process. The EMBO Journal 21, 38813887.Google Scholar
Brookman, K. W., Lamerdin, J. E., Thelen, M. P., Hwang, M., Reardon, J. T., Sancar, A., Zhou, Z. Q., Walter, C. A., Parris, C. N. & Thompson, L. H. (1996). ERCC4 (XPF) encodes a human nucleotide excision repair protein with eukaryotic recombination homologs. Molecular and Cellular Biology 16, 65536562.Google Scholar
Brooks, P. J., Wise, D. S., Berry, D. A., Kosmoski, J. V., Smerdon, M. J., Somers, R. L., Mackie, H., Spoonde, A. Y., Ackerman, E. J., Coleman, K., Tarone, R. E. & Robbins, J. H. (2000). The oxidative DNA lesion 8,5′-(S)-cyclo-2′-deoxyadenosine is repaired by the nucleotide excision repair pathway and blocks gene expression in mammalian cells. The Journal of Biological Chemistry 275, 2235522362.CrossRefGoogle ScholarPubMed
Buchko, G. W., Ni, S., Thrall, B. D. & Kennedy, M. A. (1998). Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA. Nucleic Acids Research 26, 27792788.Google Scholar
Buchko, G. W., Tung, C. S., McAteer, K., Isern, N. G., Spicer, L. D. & Kennedy, M. A. (2001). DNA-XPA interactions: a 31P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA. Nucleic Acids Research 29, 26352643.CrossRefGoogle ScholarPubMed
Buechner, C. N., Heil, K., Michels, G., Carell, T., Kisker, C. & Tessmer, I. (2014). Strand-specific recognition of DNA damages by XPD provides insights into nucleotide excision repair substrate versatility. The Journal of Biological Chemistry 289, 36133624.CrossRefGoogle ScholarPubMed
Burns, J. L., Guzder, S. N., Sung, P., Prakash, S. & Prakash, L. (1996). An affinity of human replication protein A for ultraviolet-damaged DNA. The Journal of Biological Chemistry 271, 1160711610.Google Scholar
Buschta-Hedayat, N., Buterin, T., Hess, M. T., Missura, M. & Naegeli, H. (1999). Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA. Proceedings of the National Academy of Sciences of the United States of America 96, 60906095.CrossRefGoogle ScholarPubMed
Buterin, T., Hess, M. T., Luneva, N., Geacintov, N. E., Amin, S., Kroth, H., Seidel, A. & Naegeli, H. (2000). Unrepaired Fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots. Cancer Research 60, 18491856.Google Scholar
Camenisch, U., Dip, R., Schumacher, S. B., Schuler, B. & Naegeli, H. (2006). Recognition of helical kinks by xeroderma pigmentosum group A protein triggers DNA excision repair. Nature Structural and Molecular Biology 13, 278284.CrossRefGoogle ScholarPubMed
Camenisch, U. & Nägeli, H. (2008). XPA gene, its product and biological roles. Advances in Experimental Medicine and Biology 637, 2838.Google Scholar
Camenisch, U., Trautlein, D., Clement, F., Fei, J., Leitenstorfer, A., Ferrando- May, E. & Naegeli, H. (2009). Two-stage dynamic DNA quality check by xeroderma pigmentosum group C protein. EMBO Journal 28, 23872399.Google Scholar
Chen, X., Velmurugu, Y., Zheng, G., Park, B., Shim, Y., Kim, Y., Liu, L., Van Houten, B., He, C., Ansaria, A. & Min, J. (2015). Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nature Communications 6, 5849.Google Scholar
Chu, G. & Chang, E. (1988). Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA. Science 242, 564567.Google Scholar
Citterio, E., Van Den Boom, V., Schnitzler, G., Kanaar, R., Bonte, E., Kingston, R. E., Hoeijmakers, J. H. & Vermeulen, W. (2000). ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor. Molecular and Cellular Biology 20, 76437653.Google Scholar
Cleaver, J. E. (2000). Common pathways for ultraviolet skin carcinogenesis in the repair and replication defective groups of xeroderma pigmentosum. Journal of Dermatological Science 23, 111.CrossRefGoogle ScholarPubMed
Cleaver, J. E., Lam, E. T. & Revet, I. (2009). Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity. Nature Reviews Genetics 10, 756768.Google Scholar
Cleaver, J. E. & States, J. C. (1997). The DNA damage-recognition problem in human and other eukaryotic cells: the XPA damage binding protein. Biochemical Journal 328, 112.Google Scholar
Coin, F., Marinoni, J. C., Rodolfo, C., Fribourg, S., Pedrini, A. M. & Egly, J. M. (1998). Mutations in the XPD helicase gene result in XP and TTD phenotypes, preventing interaction between XPD and the p44 subunit of TFIIH. Nature Genetics 20, 184188.Google Scholar
Coin, F., Oksenych, V. & Egly, J. M. (2007). Distinct roles for the XPB/p52 and XPD/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair. Molecular Cell 26, 245256.CrossRefGoogle ScholarPubMed
Coin, F., Oksenych, V., Mocquet, V., Groh, S., Blattner, C. & Egly, J. M. (2008). Nucleotide excision repair driven by the dissociation of CAK from TFIIH. Molecular Cell 31, 920.Google Scholar
Constantinou, A., Gunz, D., Evans, E., Lalle, P., Bates, P. A., Wood, R. D. & Clarkson, S. G. (1999). Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair. The Journal of Biological Chemistry 274, 56375648.Google Scholar
Cordonnier, A. M., Lehmann, A. R. & Fuchs, R. P. (1999). Impaired translesion synthesis in xeroderma pigmentosum variant extracts. Molecular and Cellular Biology 19, 22062211.Google Scholar
Das, D., Folkers, G. E., van Dijk, M., Jaspers, N. G., Hoeijmakers, J. H., Kaptein, R. & Boelens, R. (2012). The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition. Structure 20, 667675.CrossRefGoogle Scholar
Das, D., Tripsianes, K., Jaspers, N. G., Hoeijmakers, J. H., Kaptein, R., Boelens, R. & Folkers, G. E. (2008). The HhH domain of the human DNA repair protein XPF forms stable homodimers. Proteins 70, 15511563.Google Scholar
de Laat, W. L., Appeldoorn, E., Sugasawa, K., Weterings, E., Jaspers, N. G. J. & Hoeijmakers, J. H. J. (1998). DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes & Development 12, 25982609.Google Scholar
de Laat, W. L., Jaspers, N. G. & Hoeijmakers, J. H. (1999). Molecular mechanism of nucleotide excision repair. Genes & Development 13, 768785.Google Scholar
De Weerd-Kastelein, E. A., Keijzer, W. & Bootsma, D. (1972). Genetic heterogeneity of xeroderma pigmentosum demonstrated by somatic cell hybridization. Nature: New Biology 238, 8083.Google ScholarPubMed
Demple, B. & Harrison, L. (1994). Repair of oxidative damage to DNA: enzymology and biology. Annual Review of Biochemistry 63, 915948.Google Scholar
Donahue, B. A., Yin, S., Taylor, J. S., Reines, D. & Hanawalt, P. C. (1994). Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template. Proceedings of the National Academy of Sciences of the United States of America 91, 85028506.Google Scholar
Dubaele, S., Proietti De Santis, L., Bienstock, R. J., Keriel, A., Stefanini, M., Van Houten, B. & Egly, J. M. (2003). Basal transcription defect discriminates between xeroderma pigmentosum and trichothiodystrophy in XPD patients. Molecular Cell 11, 16351646.Google Scholar
Dunand-Sauthier, I., Hohl, M., Thorel, F., Jaquier-Gubler, P., Clarkson, S. G. & Scharer, O. D. (2005). The spacer region of XPG mediates recruitment to nucleotide excision repair complexes and determines substrate specificity. The Journal of Biological Chemistry 280, 70307037.Google Scholar
Edenberg, H. & Hanawalt, P. (1972). Size of repair patches in the DNA of ultraviolet-irradiated HeLa cells. Biochimica et Biophysica Acta 272, 361372.Google Scholar
El-Mahdy, M. A., Zhu, Q., Wang, Q. E., Wani, G., Praetorius-Ibba, M., Wani, A. A. (2006). Cullin 4A-mediated proteolysis of DDB2 protein at DNA damage sites regulates in vivo lesion recognition by XPC. Journal of Biological Chemistry 281, 1340413411.Google Scholar
Evans, E., Fellows, J., Coffer, A. & Wood, R. D. (1997a). Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein. The EMBO Journal 16, 625638.Google Scholar
Evans, E., Moggs, J. G., Hwang, J. R., Egly, J. M. & Wood, R. D. (1997b). Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. The EMBO Journal 16, 65596573.Google Scholar
Fagbemi, A. F., Orelli, B. & Scharer, O. D. (2011). Regulation of endonuclease activity in human nucleotide excision repair. DNA Repair 10, 722729.CrossRefGoogle ScholarPubMed
Fan, L., Arvai, A. S., Cooper, P. K., Iwai, S., Hanaoka, F. & Tainer, J. A. (2006). Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Molecular Cell 22, 2737.CrossRefGoogle ScholarPubMed
Fan, L., Fuss, J. O., Cheng, Q. J., Arvai, A. S., Hammel, M., Roberts, V. A., Cooper, P. K. & Tainer, J. A. (2008). XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell 133, 789800.Google Scholar
Feltes, B. C. & Bonatto, D. (2015). Overview of xeroderma pigmentosum proteins architecture, mutations and post-translational modifications. Mutation Research/Reviews in Mutation Research 763, 306320.Google Scholar
Fischer, E. S., Scrima, A., Bohm, K., Matsumoto, S., Lingaraju, G. M., Faty, M., Yasuda, T., Cavadini, S., Wakasugi, M., Hanaoka, F., Iwai, S., Gut, H., Sugasawa, K. & Thoma, N. H. (2011). The molecular basis of CRL4DDB2/CSA ubiquitin ligase architecture, targeting, and activation. Cell 147, 10241039.Google Scholar
Fitch, M. E., Nakajima, S., Yasui, A. & Ford, J. M. (2003). In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimers by the DDB2 gene product. The Journal of Biological Chemistry 278, 4690646910.Google Scholar
Friedberg, E. C. (1995). DNA Repair and Mutagenesis. Waschington, D.C: ASM Press.Google Scholar
Friedberg, E. C. (2001). How nucleotide excision repair protects against cancer. Nature Review Cancer 1, 2233.Google Scholar
Friedberg, E. C. (2005). Suffering in silence: the tolerance of DNA damage. Nature Reviews Molecular Cell Biology 6, 943953.Google Scholar
Fujiwara, Y., Masutani, C., Mizukoshi, T., Kondo, J., Hanaoka, F. & Iwai, S. (1999). Characterization of DNA recognition by the human UV-damaged DNA-binding protein. The Journal of Biological Chemistry 274, 2002720033.CrossRefGoogle ScholarPubMed
Fuss, J. O. & Tainer, J. A. (2011). XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair 10, 697713.Google Scholar
Geacintov, N. E., Broyde, S., Buterin, T., Naegeli, H., Wu, M., Yan, S. & Patel, D. J. (2002). Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery. Biopolymers 65, 202210.Google Scholar
Gillet, L. C., Alzeer, J. & Scharer, O. D. (2005). Site-specific incorporation of N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-AAF) into oligonucleotides using modified ‘ultra-mild’ DNA synthesis. Nucleic Acids Research 33, 19611969.Google Scholar
Gillet, L. C. & Scharer, O. D. (2006). Molecular mechanisms of mammalian global genome nucleotide excision repair. Chemical Reviews 106, 253276.Google Scholar
Groisman, R., Polanowska, J., Kuraoka, I., Sawada, J., Saijo, M., Drapkin, R., Kisselev, A. F., Tanaka, K., Nakatani, Y. (2003). The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage. Cell 113, 357367.Google Scholar
Gunz, D., Hess, M. T. & Naegeli, H. (1996). Recognition of DNA adducts by human nucleotide excision repair. Evidence for a thermodynamic probing mechanism. The Journal of Biological Chemistry 271, 2508925098.CrossRefGoogle ScholarPubMed
Guzder, S. N., Sung, P., Bailly, V., Prakash, L. & Prakash, S. (1994). RAD25 is a DNA helicase required for DNA repair and RNA polymerase II transcription. Nature 369, 578581.Google Scholar
Hanawalt, P. C. & Spivak, G. (2008). Transcription-coupled DNA repair: two decades of progress and surprises. Nature Reviews Molecular Cell Biology 9, 958970.Google Scholar
Haracska, L., Yu, S. L., Johnson, R. E., Prakash, L. & Prakash, S. (2000). Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta. Nature Genetics 25, 458461.Google Scholar
He, Z., Henricksen, L. A., Wold, M. S. & Ingles, C. J. (1995). RPA involvement in the damage-recognition and incision steps of nucleotide excision repair. Nature 374, 566569.Google Scholar
Hebra, F. & Kaposi, M. (1874). On diseases of the skin including the exanthemata. The New Sydenham Society 61, 252258.Google Scholar
Hess, M. T., Gunz, D., Luneva, N., Geacintov, N. E. & Naegeli, H. (1997a). Base pair conformation-dependent excision of benzo[a]pyrene diol epoxide-guanine adducts by human nucleotide excision repair enzymes. Molecular and Cellular Biology 17, 70697076.Google Scholar
Hess, M. T., Gunz, D. & Naegeli, H. (1996a). A repair competition assay to assess recognition by human nucleotide excision repair. Nucleic Acids Research 24, 824828.Google Scholar
Hess, M. T., Schwitter, U., Petretta, M., Giese, B. & Naegeli, H. (1996b). Site-specific DNA substrates for human excision repair: comparison between deoxyribose and base adducts. Chemical Biology 3, 121128.Google Scholar
Hess, M. T., Schwitter, U., Petretta, M., Giese, B. & Naegeli, H. (1997b). Bipartite substrate discrimination by human nucleotide excision repair. Proceedings of the National Academy of Sciences of the United States of America 94, 66646669.Google Scholar
Hess, N. J., Buchko, G. W., Conradson, S. D., Espinosa, F. J., Ni, S., Thrall, B. D. & Kennedy, M. A. (1998). Human nucleotide excision repair protein XPA: extended X-ray absorption fine-structure evidence for a metal-binding domain. Protein Science 7, 19701975.Google Scholar
Hey, T., Lipps, G., Sugasawa, K., Iwai, S., Hanaoka, F. & Krauss, G. (2002). The XPC-HR23B complex displays high affinity and specificity for damaged DNA in a true-equilibrium fluorescence assay. Biochemistry 41, 65836587.Google Scholar
Hilario, E., Li, Y., Nobumori, Y., Liu, X. & Fan, L. (2013). Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE. Acta Crystallographica D: Biological Crystallography 69, 237246.Google Scholar
Hoeijmakers, J. H. (2001). Genome maintenance mechanisms for preventing cancer. Nature 411, 366374.Google Scholar
Hohl, M., Dunand-Sauthier, I., Staresincic, L., Jaquier-Gubler, P., Thorel, F., Modesti, M., Clarkson, S. G. & Scharer, O. D. (2007). Domain swapping between FEN-1 and XPG defines regions in XPG that mediate nucleotide excision repair activity and substrate specificity. Nucleic Acids Research 35, 30533063.Google Scholar
Hohl, M., Thorel, F., Clarkson, S. G. & Scharer, O. D. (2003). Structural determinants for substrate binding and catalysis by the structure-specific endonuclease XPG. The Journal of Biological Chemistry 278, 1950019508.Google Scholar
Hoogstraten, D., Nigg, A. L., Heath, H., Mullenders, L. H., van Driel, R., Hoeijmakers, J. H., Vermeulen, W. & Houtsmuller, A. B. (2002). Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo . Molecular Cell 10, 11631174.Google Scholar
Hosfield, D. J., Mol, C. D., Shen, B. & Tainer, J. A. (1998). Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell 95, 135146.Google Scholar
Houle, J. F. & Friedberg, E. C. (1999). The Drosophila ortholog of the human XPG gene. Gene 234, 353360.CrossRefGoogle ScholarPubMed
Houtsmuller, A. B., Rademakers, S., Nigg, A. L., Hoogstraten, D., Hoeijmakers, J. H. & Vermeulen, W. (1999). Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284, 958961.Google Scholar
Huang, J. C., Hsu, D. S., Kazantsev, A. & Sancar, A. (1994). Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts. Proceedings of the National Academy of Sciences of the United States of America 91, 1221312217.CrossRefGoogle ScholarPubMed
Hwang, B. J., Ford, J. M., Hanawalt, P. C. & Chu, G. (1999). Expression of the p48 xeroderma pigmentosum gene is p53-dependent and is involved in global genomic repair. Proceedings of the National Academy of Sciences of the United States of America 96, 424428.Google Scholar
Hwang, B. J., Toering, S., Francke, U. & Chu, G. (1998a). p48 Activates a UV-damaged-DNA binding factor and is defective in xeroderma pigmentosum group E cells that lack binding activity. Molecular and Cellular Biology 18, 43914399.Google Scholar
Hwang, K. Y., Baek, K., Kim, H. Y. & Cho, Y. (1998b). The crystal structure of flap endonuclease-1 from Methanococcus jannaschii . Nature Structural & Molecular Biology 5, 707713.Google Scholar
Ikegami, T., Kuraoka, I., Saijo, M., Kodo, N., Kyogoku, Y., Morikawa, K., Tanaka, K. & Shirakawa, M. (1998). Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA. Nature Structural & Molecular Biology 5, 701706.Google Scholar
Isaacs, R. J. & Spielmann, H. P. (2004). A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility. DNA Repair 3, 455464.Google Scholar
Iyer, N., Reagan, M. S., Wu, K. J., Canagarajah, B. & Friedberg, E. C. (1996). Interactions involving the human RNA polymerase II transcription/nucleotide excision repair complex TFIIH, the nucleotide excision repair protein XPG, and Cockayne syndrome group B (CSB) protein. Biochemistry 35, 21572167.Google Scholar
Johnson, R. E., Washington, M. T., Haracska, L., Prakash, S. & Prakash, L. (2000). Eukaryotic polymerases iota and zeta act sequentially to bypass DNA lesions. Nature 406, 10151019.Google Scholar
Jones, C. J. & Wood, R. D. (1993). Preferential binding of the xeroderma pigmentosum group A complementing protein to damaged DNA. Biochemistry 32, 1209612104.Google Scholar
Kamiuchi, S., Saijo, M., Citterio, E., de Jager, M., Hoeijmakers, J. H. & Tanaka, K. (2002). Translocation of Cockayne syndrome group A protein to the nuclear matrix: possible relevance to transcription-coupled DNA repair. Proceedings of the National Academy of Sciences of the United States of America 99, 201206.Google Scholar
Katsumi, S., Kobayashi, N., Imoto, K., Nakagawa, A., Yamashina, Y., Muramatsu, T., Shirai, T., Miyagawa, S., Sugiura, S., Hanaoka, F., Matsunaga, T., Nikaido, O. & Mori, T. (2001). In situ visualization of ultraviolet-light-induced DNA damage repair in locally irradiated human fibroblasts. Journal of Investigative Dermatology 117, 11561161.Google Scholar
Keeney, S., Chang, G. J. & Linn, S. (1993). Characterization of a human DNA damage binding protein implicated in xeroderma pigmentosum E. The Journal of Biological Chemistry 268, 2129321300.Google Scholar
Kim, T. K., Ebright, R. H. & Reinberg, D. (2000). Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 288, 14181422.Google Scholar
Kobayashi, T., Takeuchi, S., Saijo, M., Nakatsu, Y., Morioka, H., Otsuka, E., Wakasugi, M., Nikaido, O. & Tanaka, K. (1998). Mutational analysis of a function of xeroderma pigmentosum group A (XPA) protein in strand-specific DNA repair. Nucleic Acids Research 26, 46624668.Google Scholar
Koch, S. C., Kuper, J., Gasteiger, K. L., Simon, N., Strasser, R., Eisen, D., Geiger, S., Schneider, S., Kisker, C. & Carell, T. (2015). Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA). Proceedings of the National Academy of Sciences of the United States of America 112, 82728277.Google Scholar
Kondratick, C. M., Washington, M. T., Prakash, S. & Prakash, L. (2001). Acidic residues critical for the activity and biological function of yeast DNA polymerase eta. Molecular and Cellular Biology 21, 20182025.Google Scholar
Kuper, J., Braun, C., Elias, A., Michels, G., Sauer, F., Schmitt, D. R., Poterszman, A., Egly, J. M. & Kisker, C. (2014). In TFIIH, XPD helicase is exclusively devoted to DNA repair. PLoS Biology 12, e1001954.Google Scholar
Kuper, J., Wolski, S. C., Michels, G. & Kisker, C. (2012). Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation. The EMBO Journal 31, 494502.Google Scholar
Kuraoka, I., Morita, E. H., Saijo, M., Matsuda, T., Morikawa, K., Shirakawa, M. & Tanaka, K. (1996). Identification of a damaged-DNA binding domain of the XPA protein. Mutation Research 362, 8795.Google Scholar
Kusumoto, R., Masutani, C., Sugasawa, K., Iwai, S., Araki, M., Uchida, A., Mizukoshi, T. & Hanaoka, F. (2001). Diversity of the damage recognition step in the global genomic nucleotide excision repair in vitro . Mutation Research 485, 219227.Google Scholar
Lehmann, A. R. (2001). The xeroderma pigmentosum group D (XPD) gene: one gene, two functions, three diseases. Genes & Development 15, 1523.Google Scholar
Lehmann, A. R. (2003). DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Biochimie 85, 11011111.Google Scholar
Lehmann, A. R. (2008). XPD structure reveals its secrets. DNA Repair 7, 19121915.Google Scholar
Lehmann, A. R., Kirk-Bell, S., Arlett, C. F., Paterson, M. C., Lohman, P. H., de Weerd-Kastelein, E. A. & Bootsma, D. (1975). Xeroderma pigmentosum cells with normal levels of excision repair have a defect in DNA synthesis after UV-irradiation. Proceedings of the National Academy of Sciences of the United States of America 72, 219223.Google Scholar
Li, L., Elledge, S. J., Peterson, C. A., Bales, E. S. & Legerski, R. J. (1994). Specific association between the human DNA repair proteins XPA and ERCC1. Proceedings of the National Academy of Sciences of the United States of America 91, 50125016.Google Scholar
Li, C., Golebiowski, F. M., Onishi, Y., Samara, N. L., Sugasawa, K. & Yang, W. (2015). Tripartite DNA lesion recognition and verification by XPC, TFIIH, and XPA in nucleotide excision repair. Molecular Cell 59, 10251034.Google Scholar
Li, L., Lu, X., Peterson, C. A. & Legerski, R. J. (1995a). An interaction between the DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair. Molecular and Cellular Biology 15, 53965402.Google Scholar
Li, L., Peterson, C. A., Lu, X. & Legerski, R. J. (1995b). Mutations in XPA that prevent association with ERCC1 are defective in nucleotide excision repair. Molecular and Cellular Biology 15, 19931998.Google Scholar
Lieber, M. R. (1997). The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair. BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 19, 233240.Google Scholar
Liu, H., Rudolf, J., Johnson, K. A., McMahon, S. A., Oke, M., Carter, L., McRobbie, A. M., Brown, S. E., Naismith, J. H. & White, M. F. (2008). Structure of the DNA repair helicase XPD. Cell 133, 801812.Google Scholar
Liu, Y., Yang, Z., Utzat, C., Wang, G., Basu, A. K. & Zou, Y. (2005). Cooperative interaction of human XPA stabilizes and enhances specific binding of XPA to DNA damage. Biochemistry 44, 73617368.Google Scholar
Livneh, Z. (2001). DNA damage control by novel DNA polymerases: translesion replication and mutagenesis. The Journal of Biological Chemistry 276, 2563925642.Google Scholar
Luijsterburg, M. S., Goedhart, J., Moser, J., Kool, H., Geverts, B., Houtsmuller, A. B., Mullenders, L. H., Vermeulen, W. & Van Driel, R. (2007). Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC. Journal of Cell Science 120, 27062716.Google Scholar
Luijsterburg, M. S., von Bornstaedt, G., Gourdin, A. M., Politi, A. Z., Mone, M. J., Warmerdam, D. O., Goedhart, J., Vermeulen, W., van Driel, R. & Hofer, T. (2010). Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair. The Journal of Cell Biology 189, 445463.Google Scholar
Lukin, M. & de Los Santos, C. (2006). NMR structures of damaged DNA. Chemical Reviews 106, 607686.Google Scholar
Maillard, O., Solyom, S. & Naegeli, H. (2007). An aromatic sensor with aversion to damaged strands confers versatility to DNA repair. PLoS Biology 5(4), e79.Google Scholar
Maltseva, E. A., Rechkunova, N. I., Gillet, L. C., Petruseva, I. O., Scharer, O. D. & Lavrik, O. I. (2007). Crosslinking of the NER damage recognition proteins XPC-HR23B, XPA and RPA to photoreactive probes that mimic DNA damages. Biochimica et Biophysica Acta 1770, 781789.Google Scholar
Masutani, C., Araki, M., Yamada, A., Kusumoto, R., Nogimori, T., Maekawa, T., Iwai, S. & Hanaoka, F. (1999a). Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity. The EMBO Journal 18, 34913501.Google Scholar
Masutani, C., Kusumoto, R., Iwai, S. & Hanaoka, F. (2000). Mechanisms of accurate translesion synthesis by human DNA polymerase eta. The EMBO Journal 19, 31003109.Google Scholar
Masutani, C., Kusumoto, R., Yamada, A., Dohmae, N., Yokoi, M., Yuasa, M., Araki, M., Iwai, S., Takio, K. & Hanaoka, F. (1999b). The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta. Nature 399, 700704.Google Scholar
Mathieu, N., Kaczmarek, N. & Naegeli, H. (2010). Strand- and site-specific DNA lesion demarcation by the xeroderma pigmentosum group D helicase. Proceedings of the National Academy of Sciences of the United States of America 107, 1754517550.Google Scholar
Mathieu, N., Kaczmarek, N., Ruthemann, P., Luch, A. & Naegeli, H. (2013). DNA quality control by a lesion sensor pocket of the xeroderma pigmentosum group D helicase subunit of TFIIH. Current Biology 23, 204212.Google Scholar
Matsuda, T., Bebenek, K., Masutani, C., Hanaoka, F. & Kunkel, T. A. (2000). Low fidelity DNA synthesis by human DNA polymerase-eta. Nature 404, 10111013.Google Scholar
Mellon, I., Spivak, G. & Hanawalt, P. C. (1987). Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell 51, 241249.Google Scholar
Mietus, M., Nowak, E., Jaciuk, M., Kustosz, P., Studnicka, J. & Nowotny, M. (2014). Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic Acids Research 42, 1076210775.Google Scholar
Min, J. H. & Pavletich, N. P. (2007). Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature 449, 570575.Google Scholar
Missura, M., Buterin, T., Hindges, R., Hubscher, U., Kasparkova, J., Brabec, V. & Naegeli, H. (2001). Double-check probing of DNA bending and unwinding by XPA-RPA: an architectural function in DNA repair. The EMBO Journal 20, 35543564.Google Scholar
Mitchell, D. L. & Nairn, R. S. (1989). The biology of the (6–4) photoproduct. Photochemistry and Photobiology 49, 805819.Google Scholar
Miyamoto, I., Miura, N., Niwa, H., Miyazaki, J. & Tanaka, K. (1992). Mutational analysis of the structure and function of the xeroderma pigmentosum group A complementing protein. Identification of essential domains for nuclear localization and DNA excision repair. The Journal of Biological Chemistry 267, 1218212187.Google Scholar
Moggs, J. G., Szymkowski, D. E., Yamada, M., Karran, P. & Wood, R. D. (1997). Differential human nucleotide excision repair of paired and mispaired cisplatin-DNA adducts. Nucleic Acids Research 25, 480491.Google Scholar
Moggs, J. G., Yarema, K. J., Essigmann, J. M. & Wood, R. D. (1996). Analysis of incision sites produced by human cell extracts and purified proteins during nucleotide excision repair of a 1,3-intrastrand d(GpTpG)-cisplatin adduct. The Journal of Biological Chemistry 271, 71777186.Google Scholar
Mone, M. J., Volker, M., Nikaido, O., Mullenders, L. H., van Zeeland, A. A., Verschure, P. J., Manders, E. M. & van Driel, R. (2001). Local UV-induced DNA damage in cell nuclei results in local transcription inhibition. EMBO Reports 2, 10131017.Google Scholar
Morikawa, K. & Shirakawa, M. (2000). Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA. Mutation Research 460, 257275.Google Scholar
Morita, E. H., Ohkubo, T., Kuraoka, I., Shirakawa, M., Tanaka, K. & Morikawa, K. (1996). Implications of the zinc-finger motif found in the DNA-binding domain of the human XPA protein. Genes to Cells 1, 437442.Google Scholar
Moser, J., Kool, H., Giakzidis, J., Caldecott, K., Mullenders, L. & Fousteri, M. I. (2001). Sealing of Chromosomal DNA Nicks during Nucleotide Excision Repair Requires XRCC1 and DNA Ligase IIIα in a cell-cycle-specific manner. Molecular Cells 27, 311323.Google Scholar
Moser, J., Kool, H., Giakzidis, I., Caldecott, K., Mullenders, L. H. & Fousteri, M. I. (2007). Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase III alpha in a cell-cycle-specific manner. Molecular Cell 27(2), 311323.Google Scholar
Mu, D., Bertrand-Burggraf, E., Huang, J. C., Fuchs, R. P., Sancar, A. & Fuchs, B. P. (1994). Human and E. coli excinucleases are affected differently by the sequence context of acetylaminofluorene-guanine adduct. Nucleic Acids Research 22, 48694871.Google Scholar
Mu, D., Park, C. H., Matsunaga, T., Hsu, D. S., Reardon, J. T. & Sancar, A. (1995). H reconstitution of human DNA repair excision nuclease in a highly defined system. Journal of Biological Chemistry 270, 24152418.Google Scholar
Naegeli, H., Bardwell, L. & Friedberg, E. C. (1992). The DNA helicase and adenosine triphosphatase activities of yeast Rad3 protein are inhibited by DNA damage. A potential mechanism for damage-specific recognition. The Journal of Biological Chemistry 267, 392398.Google Scholar
Naegeli, H., Modrich, P. & Friedberg, E. C. (1993). The DNA helicase activities of Rad3 protein of Saccharomyces cerevisiae and helicase II of Escherichia coli are differentially inhibited by covalent and noncovalent DNA modifications. The Journal of Biological Chemistry 268, 1038610392.Google Scholar
Naegeli, H. & Sugasawa, K. (2011). The xeroderma pigmentosum pathway: decision tree analysis of DNA quality. DNA Repair 10, 673683.Google Scholar
Newman, M., Murray-Rust, J., Lally, J., Rudolf, J., Fadden, A., Knowles, P. P., White, M. F. & McDonald, N. Q. (2005). Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition. The EMBO Journal 24, 895905.Google Scholar
Nichols, A. F., Ong, P. & Linn, S. (1996). Mutations specific to the xeroderma pigmentosum group E Ddb-phenotype. The Journal of Biological Chemistry 271, 2431724320.Google Scholar
Nishino, T., Komori, K., Ishino, Y. & Morikawa, K. (2003). X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: similarity between its endonuclease domain and restriction enzymes. Structure 11, 445457.Google Scholar
Nocentini, S., Coin, F., Saijo, M., Tanaka, K. & Egly, J. M. (1997). DNA damage recognition by XPA protein promotes efficient recruitment of transcription factor II H. The Journal of Biological Chemistry 272, 2299122994.CrossRefGoogle ScholarPubMed
O'Donovan, A., Davies, A. A., Moggs, J. G., West, S. C. & Wood, R. D. (1994a). XPG endonuclease makes the 3′ incision in human DNA nucleotide excision repair. Nature 371, 432435.Google Scholar
O'Donovan, A., Scherly, D., Clarkson, S. G. & Wood, R. D. (1994b). Isolation of active recombinant XPG protein, a human DNA repair endonuclease. The Journal of Biological Chemistry 269, 1596515968.Google Scholar
Ogi, T., Limsirichaikul, S., Overmeer, R. M., Volker, M., Takenaka, K., Cloney, R., Nakazawa, Y., Niimi, A., Miki, Y., Jaspers, N. G., Mullenders, L. H., Yamashita, S., Fousteri, M. I. & Lehmann, A. R. (2010). Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells. Molecular Cell 37(5), 714727.Google Scholar
Ohmori, H., Friedberg, E. C., Fuchs, R. P., Goodman, M. F., Hanaoka, F., Hinkle, D., Kunkel, T. A., Lawrence, C. W., Livneh, Z., Nohmi, T., Prakash, L., Prakash, S., Todo, T., Walker, G. C., Wang, Z. & Woodgate, R. (2001). The Y-family of DNA polymerases. Molecular Cell 8, 78.Google Scholar
Oksenych, V., Bernardes de Jesus, B., Zhovmer, A., Egly, J. M. & Coin, F. (2009). Molecular insights into the recruitment of TFIIH to sites of DNA damage. The EMBO Journal 28, 29712980.Google Scholar
Orans, J., McSweeney, E. A., Iyer, R. R., Hast, M. A., Hellinga, H. W., Modrich, P. & Beese, L. S. (2011). Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family. Cell 145, 212223.Google Scholar
Park, C. H., Bessho, T., Matsunaga, T. & Sancar, A. (1995a). Purification and characterization of the XPF-ERCC1 complex of human DNA repair excision nuclease. The Journal of Biological Chemistry 270, 2265722660.Google Scholar
Park, C. H., Mu, D., Reardon, J. T. & Sancar, A. (1995b). The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein independent of the TFIIE transcription factor. The Journal of Biological Chemistry 270, 48964902.Google Scholar
Park, C. H. & Sancar, A. (1994). Formation of a ternary complex by human XPA, ERCC1, and ERCC4 (XPF) excision repair proteins. Proceedings of the National Academy of Sciences of the United States of America 91, 50175021.Google Scholar
Pugh, R. A., Wu, C. G. & Spies, M. (2012). Regulation of translocation polarity by helicase domain 1 in SF2B helicases. The EMBO Journal 31, 503514.Google Scholar
Rademakers, S., Volker, M., Hoogstraten, D., Nigg, A. L., Mone, M. J., Van Zeeland, A. A., Hoeijmakers, J. H., Houtsmuller, A. B. & Vermeulen, W. (2003). Xeroderma pigmentosum group A protein loads as a separate factor onto DNA lesions. Molecular and Cellular Biology 23, 57555767.Google Scholar
Rajski, S. R., Jackson, B. A. & Barton, J. K. (2000). DNA repair: models for damage and mismatch recognition. Mutation Research 447, 4972.Google Scholar
Raoul, S., Bardet, M. & Cadet, J. (1995). Gamma irradiation of 2′-deoxyadenosine in oxygen-free aqueous solutions: identification and conformational features of formamidopyrimidine nucleoside derivatives. Chemical Research in Toxicology 8, 924933.Google Scholar
Read, C. M., Cary, P. D., Crane-Robinson, C., Driscoll, P. C. & Norman, D. G. (1993). Solution structure of a DNA-binding domain from HMG1. Nucleic Acids Research 21, 34273436.CrossRefGoogle ScholarPubMed
Reardon, J. T., Nichols, A. F., Keeney, S., Smith, C. A., Taylor, J. S., Linn, S. & Sancar, A. (1993). Comparative analysis of binding of human damaged DNA-binding protein (XPE) and Escherichia coli damage recognition protein (UvrA) to the major ultraviolet photoproducts: T[c,s]T, T[t,s]T, T[6–4]T, and T[Dewar]T. The Journal of Biological Chemistry 268, 2130121308.Google Scholar
Reardon, J. T. & Sancar, A. (2002). Molecular anatomy of the human excision nuclease assembled at sites of DNA damage. Molecular and Cellular Biology 22, 59385945.Google Scholar
Reardon, J. T. & Sancar, A. (2003). Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease. Genes & Development 17, 25392551.Google Scholar
Reardon, J. T. & Sancar, A. (2005). Nucleotide excision repair. Progress in Nucleic Acid Research and Molecular Biology 79, 183235.Google Scholar
Reissner, T., Schneider, S., Schorr, S. & Carell, T. (2010). Crystal structure of a cisplatin-(1,3-GTG) cross-link within DNA polymerase eta. Angewandte Chemie International Edition 49, 30773080.Google Scholar
Riedl, T., Hanaoka, F. & Egly, J. M. (2003). The comings and goings of nucleotide excision repair factors on damaged DNA. The EMBO Journal 22, 52935303.Google Scholar
Robins, P., Jones, C. J., Biggerstaff, M., Lindahl, T. & Wood, R. D. (1991). Complementation of DNA repair in xeroderma pigmentosum group A cell extracts by a protein with affinity for damaged DNA. The EMBO Journal 10, 39133921.Google Scholar
Rupp, W. D. & Howard-Flanders, P. (1968). Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation. Journal of Molecular Biology 31, 291304.Google Scholar
Saijo, M., Kuraoka, I., Masutani, C., Hanaoka, F. & Tanaka, K. (1996). Sequential binding of DNA repair proteins RPA and ERCC1 to XPA in vitro . Nucleic Acids Research 24, 47194724.Google Scholar
Sancar, A. & Tang, M. S. (1993). Nucleotide excision repair. Photochemistry and Photobiology 57, 905921.Google Scholar
Schaeffer, L., Roy, R., Humbert, S., Moncollin, V., Vermeulen, W., Hoeijmakers, J. H., Chambon, P. & Egly, J. M. (1993). DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor. Science 260, 5863.Google Scholar
Scharer, O. D. (2013). Nucleotide excision repair in eukaryotes. Cold Spring Harbor Perspectives Biology 5, a012609.Google Scholar
Schorr, S. & Carell, T. (2010a). Mechanism of acetylaminofluorene-dG induced frameshifting by polymerase eta. Chembiochem 11, 25342537.Google Scholar
Schorr, S., Schneider, S., Lammens, K., Hopfner, K. P. & Carell, T. (2010b). Mechanism of replication blocking and bypass of Y-family polymerase ɳ by bulky acetylaminofluorene DNA adducts. Proceedings of the National Academy of Sciences of the United States of America 107, 2072020725.Google Scholar
Schweizer, U., Hey, T., Lipps, G. & Krauss, G. (1999). Photocrosslinking locates a binding site for the large subunit of human replication protein A to the damaged strand of cisplatin-modified DNA. Nucleic Acids Research 27, 31833189.Google Scholar
Scrima, A., Konickova, R., Czyzewski, B. K., Kawasaki, Y., Jeffrey, P. D., Groisman, R., Nakatani, Y., Iwai, S., Pavletich, N. P. & Thoma, N. H. (2008). Structural basis of UV DNA-damage recognition by the DDB1–DDB2 complex. Cell 135, 12131223.Google Scholar
Shin, D. S., Pellegrini, L., Daniels, D. S., Yelent, B., Craig, L., Bates, D., Yu, D. S., Shivji, M. K., Hitomi, C., Arvai, A. S., Volkmann, N., Tsuruta, H., Blundell, T. L., Venkitaraman, A. R. & Tainer, J. A. (2003). Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. The EMBO Journal 22, 45664576.Google Scholar
Shivji, M. K., Podust, V. N., Hubscher, U. & Wood, R. D. (1995). Nucleotide excision repair DNA synthesis by DNA polymerase epsilon in the presence of PCNA, RFC, and RPA. Biochemistry 34, 50115017.Google Scholar
Sijbers, A. M., de Laat, W. L., Ariza, R. R., Biggerstaff, M., Wei, Y. F., Moggs, J. G., Carter, K. C., Shell, B. K., Evans, E., de Jong, M. C., Rademakers, S., de Rooij, J., Jaspers, N. G., Hoeijmakers, J. H. & Wood, R. D. (1996). Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease. Cell 86, 811822.Google Scholar
Silverstein, T. D., Jain, R., Johnson, R. E., Prakash, L., Prakash, S. & Aggarwal, A. K. (2010a). Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase eta. Structure 18, 14631470.Google Scholar
Silverstein, T. D., Johnson, R. E., Jain, R., Prakash, L., Prakash, S. & Aggarwal, A. K. (2010b). Structural basis for the suppression of skin cancers by DNA polymerase eta. Nature 465, 10391043.Google Scholar
Singh, S., Folkers, G. E., Bonvin, A. M., Boelens, R., Wechselberger, R., Niztayev, A. & Kaptein, R. (2002). Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli. The EMBO Journal 21, 62576266.Google Scholar
Staresincic, L., Fagbemi, A. F., Enzlin, J. H., Gourdin, A. M., Wijgers, N., Dunand-Sauthier, I., Giglia-Mari, G., Clarkson, S. G., Vermeulen, W. & Scharer, O. D. (2009). Coordination of dual incision and repair synthesis in human nucleotide excision repair. The EMBO Journal 28, 11111120.Google Scholar
Story, R. M. & Steitz, T. A. (1992). Structure of the recA protein–ADP complex. Nature 355, 374376.Google Scholar
Sugasawa, K., Ng, J. M., Masutani, C., Iwai, S., van der Spek, P. J., Eker, A. P., Hanaoka, F., Bootsma, D. & Hoeijmakers, J. H. (1998). Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Molecular Cell 2, 223232.Google Scholar
Sugasawa, K., Okamoto, T., Shimizu, Y., Masutani, C., Iwai, S. & Hanaoka, F. (2001). A multistep damage recognition mechanism for global genomic nucleotide excision repair. Genes & Development 15, 507521.Google Scholar
Sugasawa, K., Okuda, Y., Saijo, M., Nishi, R., Matsuda, N., Chu, G., Mori, T., Iwai, S., Tanaka, K., Tanaka, K., Hanaoka, F. (2005). UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex. Cell 121, 387400.Google Scholar
Sugasawa, K., Shimizu, Y., Iwai, S. & Hanaoka, F. (2002). A molecular mechanism for DNA damage recognition by the xeroderma pigmentosum group C protein complex. DNA Repair 1, 95107.Google Scholar
Sugitani, N., Shell, S. M., Soss, S. E. & Chazin, W. J. (2014). Redefining the DNA-binding domain of human XPA. Journal of the American Chemical Society 136, 1083010833.Google Scholar
Sung, P., Higgins, D., Prakash, L. & Prakash, S. (1988). Mutation of lysine-48 to arginine in the yeast RAD3 protein abolishes its ATPase and DNA helicase activities but not the ability to bind ATP. The EMBO Journal 7, 32633269.Google Scholar
Sweder, K. S. & Hanawalt, P. C. (1992). Preferential repair of cyclobutane pyrimidine dimers in the transcribed strand of a gene in yeast chromosomes and plasmids is dependent on transcription. Proceedings of the National Academy of Sciences of the United States of America 89, 1069610700.Google Scholar
Takao, M., Abramic, M., Moos, M. Jr., Otrin, V. R., Wootton, J. C., McLenigan, M., Levine, A. S. & Protic, M. (1993). A 127 kDa component of a UV-damaged DNA-binding complex, which is defective in some xeroderma pigmentosum group E patients, is homologous to a slime mold protein. Nucleic Acids Research 21, 41114118.Google Scholar
Tang, J. Y., Hwang, B. J., Ford, J. M., Hanawalt, P. C. & Chu, G. (2000). Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis. Molecular Cell 5, 737744.Google Scholar
Tantin, D. (1998). RNA polymerase II elongation complexes containing the Cockayne syndrome group B protein interact with a molecular complex containing the transcription factor IIH components xeroderma pigmentosum B and p62. The Journal of Biological Chemistry 273, 2779427799.Google Scholar
Tantin, D., Kansal, A. & Carey, M. (1997). Recruitment of the putative transcription-repair coupling factor CSB/ERCC6 to RNA polymerase II elongation complexes. Molecular and Cellular Biology 17, 68036814.Google Scholar
Tapias, A., Auriol, J., Forget, D., Enzlin, J. H., Scharer, O. D., Coin, F., Coulombe, B. & Egly, J. M. (2004). Ordered conformational changes in damaged DNA induced by nucleotide excision repair factors. The Journal of Biological Chemistry 279, 1907419083.Google Scholar
Thoma, B. S. & Vasquez, K. M. (2003). Critical DNA damage recognition functions of XPC-hHR23B and XPA-RPA in nucleotide excision repair. Molecular Carcinogenesis 38, 113.Google Scholar
Thorel, F., Constantinou, A., Dunand-Sauthier, I., Nouspikel, T., Lalle, P., Raams, A., Jaspers, N. G., Vermeulen, W., Shivji, M. K., Wood, R. D. & Clarkson, S. G. (2004). Definition of a short region of XPG necessary for TFIIH interaction and stable recruitment to sites of UV damage. Molecular and Cellular Biology 24, 1067010680.Google Scholar
Tirode, F., Busso, D., Coin, F. & Egly, J. M. (1999). Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7. Molecular Cell 3, 8795.Google Scholar
Tornaletti, S. & Hanawalt, P. C. (1999). Effect of DNA lesions on transcription elongation. Biochimie 81, 139146.Google Scholar
Trincao, J., Johnson, R. E., Escalante, C. R., Prakash, S., Prakash, L. & Aggarwal, A. K. (2001). Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis. Molecular Cell 8, 417426.Google Scholar
Tripsianes, K., Folkers, G., Ab, E., Das, D., Odijk, H., Jaspers, N. G., Hoeijmakers, J. H., Kaptein, R. & Boelens, R. (2005). The structure of the human ERCC1/XPF interaction domains reveals a complementary role for the two proteins in nucleotide excision repair. Structure 13, 18491858.Google Scholar
Tripsianes, K., Folkers, G. E., Zheng, C., Das, D., Grinstead, J. S., Kaptein, R. & Boelens, R. (2007). Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization. Nucleic Acids Research 35, 57895798.Google Scholar
Tsodikov, O. V., Enzlin, J. H., Scharer, O. D. & Ellenberger, T. (2005). Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF–ERCC1. Proceedings of the National Academy of Sciences of the United States of America 102, 1123611241.Google Scholar
Tsodikov, O. V., Ivanov, D., Orelli, B., Staresincic, L., Shoshani, I., Oberman, R., Scharer, O. D., Wagner, G. & Ellenberger, T. (2007). Structural basis for the recruitment of ERCC1–XPF to nucleotide excision repair complexes by XPA. The EMBO Journal 26, 47684776.Google Scholar
Tsutakawa, S. E., Classen, S., Chapados, B. R., Arvai, A. S., Finger, L. D., Guenther, G., Tomlinson, C. G., Thompson, P., Sarker, A. H., Shen, B., Cooper, P. K., Grasby, J. A. & Tainer, J. A. (2011). Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell 145, 198211.Google Scholar
Tuteja, N. & Tuteja, R. (1996). DNA helicases: the long unwinding road. Nature Genetics 13, 1112.Google Scholar
Van der Spek, P. J., Eker, A., Rademakers, S., Visser, C., Sugasawa, K., Masutani, C., Hanaoka, F., Bootsma, D. & Hoeijmakers, J. H. (1996). XPC and human homologs of RAD23: intracellular localization and relationship to other nucleotide excision repair complexes. Nucleic Acids Research 24, 25512559.Google Scholar
Venema, J., van Hoffen, A., Karcagi, V., Natarajan, A. T., van Zeeland, A. A. & Mullenders, L. H. (1991). Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes. Molecular and Cellular Biology 11, 41284134.Google Scholar
Volker, M., Mone, M. J., Karmakar, P., van Hoffen, A., Schul, W., Vermeulen, W., Hoeijmakers, J. H., van Driel, R., van Zeeland, A. A. & Mullenders, L. H. (2001). Sequential assembly of the nucleotide excision repair factors in vivo . Molecular Cell 8, 213224.Google Scholar
Wakasugi, M., Kawashima, A., Morioka, H., Linn, S., Sancar, A., Mori, T., Nikaido, O. & Matsunaga, T. (2002). DDB accumulates at DNA damage sites immediately after UV irradiation and directly stimulates nucleotide excision repair. The Journal of Biological Chemistry 277, 16371640.Google Scholar
Wakasugi, M. & Sancar, A. (1998). Assembly, subunit composition, and footprint of human DNA repair excision nuclease. Proceedings of the National Academy of Sciences of the United States of America 95, 66696674.Google Scholar
Wakasugi, M. & Sancar, A. (1999). Order of assembly of human DNA repair excision nuclease. The Journal of Biological Chemistry 274, 1875918768.Google Scholar
Wang, M., Mahrenholz, A. & Lee, S. H. (2000). RPA stabilizes the XPA-damaged DNA complex through protein–protein interaction. Biochemistry 39, 64336439.Google Scholar
Wang, H., Zhai, L., Xu, J., Joo, H. Y., Jackson, S., Erdjument-Bromage, H., Tempst, P., Xiong, Y. & Zhang, Y. (2006). Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage. Mol. Cell 22, 383394.Google Scholar
Weir, H. M., Kraulis, P. J., Hill, C. S., Raine, A. R., Laue, E. D. & Thomas, J. O. (1993). Structure of the HMG box motif in the B-domain of HMG1. The EMBO Journal 12, 13111319.Google Scholar
White, M. F. (2009). Structure, function and evolution of the XPD family of iron-sulfur-containing 5′–>3′ DNA helicases. Biochemical Society Transactions 37, 547551.Google Scholar
Winkler, G. S., Araujo, S. J., Fiedler, U., Vermeulen, W., Coin, F., Egly, J. M., Hoeijmakers, J. H., Wood, R. D., Timmers, H. T. & Weeda, G. (2000). TFIIH with inactive XPD helicase functions in transcription initiation but is defective in DNA repair. The Journal of Biological Chemistry 275, 42584266.Google Scholar
Wolski, S. C., Kuper, J., Hanzelmann, P., Truglio, J. J., Croteau, D. L., Van Houten, B. & Kisker, C. (2008). Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD. PLoS Biology 6, e149.Google Scholar
Wood, R. D. (1997). Nucleotide excision repair in mammalian cells. The Journal of Biological Chemistry 272, 2346523468.Google Scholar
Yan, H., Yuan, W., Velculescu, V. E., Vogelstein, B. & Kinzler, K. W. (2002). Allelic variation in human gene expression. Science 297, 1143.Google Scholar
Yan, S., Wu, M., Buterin, T., Naegeli, H., Geacintov, N. E. & Broyde, S. (2003). Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide−adenine adducts†. Biochemistry 42, 23392354.Google Scholar
Yang, Z., Roginskaya, M., Colis, L. C., Basu, A. K., Shell, S. M., Liu, Y., Musich, P. R., Harris, C. M., Harris, T. M. & Zou, Y. (2006). Specific and efficient binding of xeroderma pigmentosum complementation group A to double-strand/single-strand DNA junctions with 3′- and/or 5′-ssDNA branches. Biochemistry 45, 1592115930.Google Scholar
Yang, Z. G., Liu, Y., Mao, L. Y., Zhang, J. T. & Zou, Y. (2002). Dimerization of human XPA and formation of XPA2-RPA protein complex. Biochemistry 41, 1301213020.Google Scholar
Yasui, M., Dong, H., Bonala, R. R., Suzuki, N., Ohmori, H., Hanaoka, F., Johnson, F., Grollman, A. P. & Shibutani, S. (2004). Mutagenic properties of 3-(deoxyguanosin-N2-yl)-2-acetylaminofluorene, a persistent acetylaminofluorene-derived DNA adduct in mammalian cells. Biochemistry 43, 1500515013.Google Scholar
Yeh, J. I., Levine, A. S., Du, S., Chinte, U., Ghodke, H., Wang, H., Shi, H., Hsieh, C. L., Conway, J. F., Van Houten, B. & Rapić-Otrin, V. (2012). Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. Proceedings of the National Academy of Sciences of the United States of America 109, E2737E2746.Google Scholar