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Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC.

Okuda M, Kinoshita M, Kakumu E, Sugasawa K, Nishimura Y
Structure 23 1827-1837 (2015)
Cited: 22 times
EuropePMC logo PMID: 26278177

Abstract

In global genome repair (GGR), XPC detects damaged nucleotides and recruits TFIIH complex. The small acidic region of XPC binds to the pleckstrin homology (PH) domain of TFIIH subunit p62; however, the recognition mechanism remains elusive. Here, we use nuclear magnetic resonance to present the tertiary structure of XPC bound to the PH domain. The XPC acidic region forms a long string stabilized by insertion of Trp133 and Val136 into two separate hollows of the PH domain, coupled with extensive electrostatic contacts. Analysis of several XPC mutants revealed that particularly Trp133 is essential for binding to the PH domain. In cell lines stably expressing mutant XPC, alanine substitution at Trp133 or Trp133/Val136 compromised UV resistance, recruitment of TFIIH to DNA damage, and removal of UV-induced photoproducts from genomic DNA. These findings show how TFIIH complex is recruited by XPC to damaged DNA, advancing our understanding of the early stage of GGR.

Reviews - 2rvb mentioned but not cited (2)

  1. Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair. Mu H, Geacintov NE, Broyde S, Yeo JE, Schärer OD. DNA Repair (Amst) 71 33-42 (2018)
  2. Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones. Okuda M, Tsunaka Y, Nishimura Y. Biophys Rev 14 1449-1472 (2022)

Articles - 2rvb mentioned but not cited (3)

  1. Structural and dynamical insights into the PH domain of p62 in human TFIIH. Okuda M, Ekimoto T, Kurita JI, Ikeguchi M, Nishimura Y. Nucleic Acids Res 49 2916-2930 (2021)
  2. Dataset for the NMR structure of the intrinsically disordered acidic region of XPC bound to the PH domain of TFIIH p62. Okuda M, Nishimura Y. Data Brief 6 571-577 (2016)
  3. Structural polymorphism of the PH domain in TFIIH. Okuda M, Nishimura Y. Biosci Rep 43 BSR20230846 (2023)


Reviews citing this publication (5)

  1. Molecular mechanisms of DNA damage recognition for mammalian nucleotide excision repair. Sugasawa K. DNA Repair (Amst) 44 110-117 (2016)
  2. The essential and multifunctional TFIIH complex. Rimel JK, Taatjes DJ. Protein Sci 27 1018-1037 (2018)
  3. Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. Tsutakawa SE, Tsai CL, Yan C, Bralić A, Chazin WJ, Hamdan SM, Schärer OD, Ivanov I, Tainer JA. DNA Repair (Amst) 96 102972 (2020)
  4. Mechanism of action of nucleotide excision repair machinery. D'Souza A, Blee AM, Chazin WJ. Biochem Soc Trans 50 375-386 (2022)
  5. XPG: a multitasking genome caretaker. Muniesa-Vargas A, Theil AF, Ribeiro-Silva C, Vermeulen W, Lans H. Cell Mol Life Sci 79 166 (2022)

Articles citing this publication (12)

  1. Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways. Okuda M, Nakazawa Y, Guo C, Ogi T, Nishimura Y. Nucleic Acids Res 45 13043-13055 (2017)
  2. Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair. van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K. Nat Commun 12 3338 (2021)
  3. Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3. Kakumu E, Nakanishi S, Shiratori HM, Kato A, Kobayashi W, Machida S, Yasuda T, Adachi N, Saito N, Ikura T, Kurumizaka H, Kimura H, Yokoi M, Sakai W, Sugasawa K. Genes Cells 22 310-327 (2017)
  4. Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail. Shimojo H, Kawaguchi A, Oda T, Hashiguchi N, Omori S, Moritsugu K, Kidera A, Hiragami-Hamada K, Nakayama J, Sato M, Nishimura Y. Sci Rep 6 22527 (2016)
  5. Functional impacts of the ubiquitin-proteasome system on DNA damage recognition in global genome nucleotide excision repair. Sakai W, Yuasa-Sunagawa M, Kusakabe M, Kishimoto A, Matsui T, Kaneko Y, Akagi JI, Huyghe N, Ikura M, Ikura T, Hanaoka F, Yokoi M, Sugasawa K. Sci Rep 10 19704 (2020)
  6. The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH. Okuda M, Araki K, Ohtani K, Nishimura Y. J Mol Biol 428 4993-5006 (2016)
  7. Three human RNA polymerases interact with TFIIH via a common RPB6 subunit. Okuda M, Suwa T, Suzuki H, Yamaguchi Y, Nishimura Y. Nucleic Acids Res 50 1-16 (2022)
  8. Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W. Nature 617 170-175 (2023)
  9. Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH. Okuda M, Higo J, Komatsu T, Konuma T, Sugase K, Nishimura Y. Biophys J 111 950-962 (2016)
  10. Histone deacetylation regulates nucleotide excision repair through an interaction with the XPC protein. Kusakabe M, Kakumu E, Kurihara F, Tsuchida K, Maeda T, Tada H, Kusao K, Kato A, Yasuda T, Matsuda T, Nakao M, Yokoi M, Sakai W, Sugasawa K. iScience 25 104040 (2022)
  11. Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA. He F, DuPrez K, Hilario E, Chen Z, Fan L. Nucleic Acids Res 48 11695-11705 (2020)
  12. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein. Le J, Min JH. J Biomol Struct Dyn 41 13535-13562 (2023)


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