1. 結構生物學期末報告 系級 生物科技所 學生 欒媄竹 學號 D93360006

2. 研究內容 NER 是生物體中 DNA 損害的主要修 補系統。而 XPA 與 RPA 在 NER 起始 的步驟中是共同作用於受損的 DNA 之 3’ 端，因此研究 XPA 和 RPA 蛋白 為分析對象進行分析。 NER 是生物體中 DNA 損害的主要修 補系統。而 XPA 與 RPA 在 NER 起始 的步驟中是共同作用於受損的 DNA 之 3’ 端，因此研究 XPA 和 RPA 蛋白 為分析對象進行分析。

3. NER Fig. Model for nucleotide excision repair of non- transcribed DNA in mammalian cells ( Batty and Wood, 2000 ).

4. XPA

5. PDB ID: 1XPA

6. RibbonsCylinders Asymmetric Unit

7. PDB ID: 1XPA

10. a, The numbering is shown for human XPA. The asterisks indicate the zinc-coordinated cysteine residues. The secondary structure of human XPA is indicated. Important residues discussed in the text are colored (green, basic; yellow, acidic; grey, hydrophobic). Sequence alignment of the central domains of XPA

11. b, Best-fit backbone superpositions of the 30 final structures of the central domain of human XPA (residues 98–210) in stereo. The backbone atoms of residues 102–155, 163–165 and 180–209 are superimposed. c, Schematic ribbon drawing of the NMR structure of the central domain of human XPA in stereo. GREEN: Loops L1 and L2 RED: b-strands GREEN: a-helices

12. Structural statistics1 for the central domain of XPA

13. a, Best-fit ackbone superpositions of the 30 final structures of the zinc- ontaining subdomain (residues 102–129). RED: hydrophobic core GREEN: zinc-binding cysteines Structures of the zinc-containing subdomain

14. RED: acidic patch GREEN: hydrophobic patch Structures of the zinc-containing subdomain

15. GREEN: hydrophobic side chains of the zinc-containing subdomain that form the core RED: C-terminal subdomain Structures of the zinc-containing subdomain

16. a, Best-fit backbone superpositions of the 30 final structures of the C-terminal subdomain (residues 138–209). The backbone atoms of the residues 138–155, 163–165 and 180–209 are superimposed. LIGHT BLUE: Loops L1 and L2RED: hydrophobic core BLUE: positive charges RED: acidic residues in helices a2 and a3 Structures of the C-terminal subdomain

17. b, Mapping of the XPA residues with chemical shift perturbation or broadening effects in the (15N, 1H) HSQC spectra. The residues of which the amide resonances were perturbed upon complex formation with the cisplatin-damaged oligonucleotide (chemical shift perturbation defined by more than 0.08 p.p.m. for 15N or 0.02 p.p.m. for 1H, or broadening defined by peak intensities decreased to <50 % of their original values) are indicated in magenta, and those of which the amide resonances showed specific broadening upon complex formation with RPA70181–422 (the peak intensities decreased to <65 % of their original values) are colored green. Distribution of the electrostatic potential on the solvent- accessible surface of the central domain of XPA BLUE: C-terminal subdomain positive potential RED: zinc-ontaining subdomain negatively potential

18. RPA

19. PDB ID: 1XPA

20. PDB ID: 1JMC

21. RibbonsCylinders Asymmetric Unit

22. PDB ID: 1JMC

23. Sequence alignment of the central domains of RPA70

24. Conclusion 脊椎動物中 XPA 蛋白序列保守性高, 具有 和, 其中後者是 與 RPA 蛋白結合共同作用, 經分析發現 呈現為 帶 的情況, 而 RPA 蛋白則為帶, 印證其 可能互相吸引而結合作用。 脊椎動物中 XPA 蛋白序列保守性高, 具有 C-terminal subdomain 和 zinc- containing subdomain, 其中後者是 與 RPA 蛋白結合共同作用, 經分析發現 zinc-containing subdomain 呈現為 帶 negatively potential 的情況, 而 RPA 蛋白則為帶 positive potential, 印證其 可能互相吸引而結合作用。

25. References

26. Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA Takahisa Ikegami 1, Isao Kuraoka 2, Masafumi Saijo 2, Naohiko Kodo 2, Yoshimasa Kyogoku 3, Kosuke Morikawa 4, Kiyoji Tanaka 2 and Masahiro Shirakawa 1 1 Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan. 2 Institute for Molecular and Cellular Biology, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565, Japan. 3 Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565, Japan. 4 Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565, Japan. Nat. Struct. Biol. 5 1998 701–706.

27. Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA Kosuke Morikawa 1, Masahiro Shirakawa 2 1 Department of Structural Biology, Biomolecular Engineering Research Institute BERI, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan 2 Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan Mutation Research 460 2000 257 – 275

28. MassSpectrometric Identification of Lysines Involved in the Interaction of Human Replication Protein A with Single-Stranded DNA Mass Spectrometric Identification of Lysines Involved in the Interaction of Human Replication Protein A with Single-Stranded DNA Steven M. Shell, ‡ Sonja Hess, § Mamuka Kvaratskhelia, | and Yue Zou *,‡ Department of Biochemistry and Molecular Biology, James H. Quillen College of Medicine, East Tennessee State UniVersity, Johnson City, Tennessee 37614, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Department of Health and Human SerVices, Bethesda, Maryland 20892, and The Ohio State UniVersity Health Sciences Center, College of Pharmacy, Center for RetroVirus Research and ComprehensiVe Cancer Center, Columbus, Ohio 43210. Biochemistry 2005, 44, 971-978