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Molecular mechanisms of xeroderma pigmentosum (XP) proteins

  • Sandra C. Koch (a1), Nina Simon (a1), Charlotte Ebert (a1) and Thomas Carell (a1)
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.

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Corresponding author
* 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
References
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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.
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.
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.
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.
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.
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.
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.
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.
Batty, D. P. & Wood, R. D. (2000b). Damage recognition in nucleotide excision repair of DNA. Gene 241, 193204.
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.
Berneburg, M. & Lehmann, A. R. (2001). Xeroderma pigmentosum and related disorders: defects in DNA repair and transcription. Advances in Genetics 43, 71102.
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.
Bootsma, D. & Hoeijmakers, J. H. (1993). DNA repair. Engagement with transcription. Nature 363, 114115.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Camenisch, U. & Nägeli, H. (2008). XPA gene, its product and biological roles. Advances in Experimental Medicine and Biology 637, 2838.
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.
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.
Chu, G. & Chang, E. (1988). Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA. Science 242, 564567.
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.
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.
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.
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.
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.
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.
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.
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.
Cordonnier, A. M., Lehmann, A. R. & Fuchs, R. P. (1999). Impaired translesion synthesis in xeroderma pigmentosum variant extracts. Molecular and Cellular Biology 19, 22062211.
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.
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.
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.
de Laat, W. L., Jaspers, N. G. & Hoeijmakers, J. H. (1999). Molecular mechanism of nucleotide excision repair. Genes & Development 13, 768785.
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.
Demple, B. & Harrison, L. (1994). Repair of oxidative damage to DNA: enzymology and biology. Annual Review of Biochemistry 63, 915948.
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.
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.
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.
Edenberg, H. & Hanawalt, P. (1972). Size of repair patches in the DNA of ultraviolet-irradiated HeLa cells. Biochimica et Biophysica Acta 272, 361372.
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.
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.
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.
Fagbemi, A. F., Orelli, B. & Scharer, O. D. (2011). Regulation of endonuclease activity in human nucleotide excision repair. DNA Repair 10, 722729.
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.
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.
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.
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.
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.
Friedberg, E. C. (1995). DNA Repair and Mutagenesis. Waschington, D.C: ASM Press.
Friedberg, E. C. (2001). How nucleotide excision repair protects against cancer. Nature Review Cancer 1, 2233.
Friedberg, E. C. (2005). Suffering in silence: the tolerance of DNA damage. Nature Reviews Molecular Cell Biology 6, 943953.
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.
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.
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.
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.
Gillet, L. C. & Scharer, O. D. (2006). Molecular mechanisms of mammalian global genome nucleotide excision repair. Chemical Reviews 106, 253276.
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.
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.
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.
Hanawalt, P. C. & Spivak, G. (2008). Transcription-coupled DNA repair: two decades of progress and surprises. Nature Reviews Molecular Cell Biology 9, 958970.
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.
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.
Hebra, F. & Kaposi, M. (1874). On diseases of the skin including the exanthemata. The New Sydenham Society 61, 252258.
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.
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.
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.
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.
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.
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.
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.
Hoeijmakers, J. H. (2001). Genome maintenance mechanisms for preventing cancer. Nature 411, 366374.
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.
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.
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.
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.
Houle, J. F. & Friedberg, E. C. (1999). The Drosophila ortholog of the human XPG gene. Gene 234, 353360.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Jones, C. J. & Wood, R. D. (1993). Preferential binding of the xeroderma pigmentosum group A complementing protein to damaged DNA. Biochemistry 32, 1209612104.
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.
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.
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.
Kim, T. K., Ebright, R. H. & Reinberg, D. (2000). Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 288, 14181422.
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.
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.
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.
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.
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.
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.
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.
Lehmann, A. R. (2001). The xeroderma pigmentosum group D (XPD) gene: one gene, two functions, three diseases. Genes & Development 15, 1523.
Lehmann, A. R. (2003). DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Biochimie 85, 11011111.
Lehmann, A. R. (2008). XPD structure reveals its secrets. DNA Repair 7, 19121915.
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.
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.
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.
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.
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.
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.
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.
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.
Livneh, Z. (2001). DNA damage control by novel DNA polymerases: translesion replication and mutagenesis. The Journal of Biological Chemistry 276, 2563925642.
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.
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.
Lukin, M. & de Los Santos, C. (2006). NMR structures of damaged DNA. Chemical Reviews 106, 607686.
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.
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.
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.
Masutani, C., Kusumoto, R., Iwai, S. & Hanaoka, F. (2000). Mechanisms of accurate translesion synthesis by human DNA polymerase eta. The EMBO Journal 19, 31003109.
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.
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.
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.
Matsuda, T., Bebenek, K., Masutani, C., Hanaoka, F. & Kunkel, T. A. (2000). Low fidelity DNA synthesis by human DNA polymerase-eta. Nature 404, 10111013.
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.
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.
Min, J. H. & Pavletich, N. P. (2007). Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature 449, 570575.
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.
Mitchell, D. L. & Nairn, R. S. (1989). The biology of the (6–4) photoproduct. Photochemistry and Photobiology 49, 805819.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Naegeli, H. & Sugasawa, K. (2011). The xeroderma pigmentosum pathway: decision tree analysis of DNA quality. DNA Repair 10, 673683.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Rajski, S. R., Jackson, B. A. & Barton, J. K. (2000). DNA repair: models for damage and mismatch recognition. Mutation Research 447, 4972.
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.
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.
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.
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.
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.
Reardon, J. T. & Sancar, A. (2005). Nucleotide excision repair. Progress in Nucleic Acid Research and Molecular Biology 79, 183235.
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.
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.
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.
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.
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.
Sancar, A. & Tang, M. S. (1993). Nucleotide excision repair. Photochemistry and Photobiology 57, 905921.
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.
Scharer, O. D. (2013). Nucleotide excision repair in eukaryotes. Cold Spring Harbor Perspectives Biology 5, a012609.
Schorr, S. & Carell, T. (2010a). Mechanism of acetylaminofluorene-dG induced frameshifting by polymerase eta. Chembiochem 11, 25342537.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Story, R. M. & Steitz, T. A. (1992). Structure of the recA protein–ADP complex. Nature 355, 374376.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Tornaletti, S. & Hanawalt, P. C. (1999). Effect of DNA lesions on transcription elongation. Biochimie 81, 139146.
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.
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.
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.
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.
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.
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.
Tuteja, N. & Tuteja, R. (1996). DNA helicases: the long unwinding road. Nature Genetics 13, 1112.
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.
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.
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.
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.
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.
Wakasugi, M. & Sancar, A. (1999). Order of assembly of human DNA repair excision nuclease. The Journal of Biological Chemistry 274, 1875918768.
Wang, M., Mahrenholz, A. & Lee, S. H. (2000). RPA stabilizes the XPA-damaged DNA complex through protein–protein interaction. Biochemistry 39, 64336439.
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.
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.
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.
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.
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.
Wood, R. D. (1997). Nucleotide excision repair in mammalian cells. The Journal of Biological Chemistry 272, 2346523468.
Yan, H., Yuan, W., Velculescu, V. E., Vogelstein, B. & Kinzler, K. W. (2002). Allelic variation in human gene expression. Science 297, 1143.
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.
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.
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.
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.
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.
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Quarterly Reviews of Biophysics
  • ISSN: 0033-5835
  • EISSN: 1469-8994
  • URL: /core/journals/quarterly-reviews-of-biophysics
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