結構生物學期末報告

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。

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. PDB ID: 1XPA Asymmetric Unit Ribbons Cylinders

7. PDB ID: 1XPA

8. PDB ID: 1XPA

9. PDB ID: 1XPA

10. Sequence alignment of the central domains of XPA 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).

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

12. Structural statistics1 for the central domain of XPA

13. Structures of the zinc-containing subdomain RED:hydrophobic core GREEN: zinc-bindingcysteines a, Best-fit ackbone superpositions of the30 final structures of the zinc-ontaining subdomain(residues 102–129).

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

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

16. Structures of the C-terminal subdomain RED: hydrophobic core LIGHT BLUE: Loops L1 and L2 BLUE: positive charges RED:acidicresidues in helices a2 and a3 a, Best-fit backbone superpositionsof the 30 final structures of the C-terminalsubdomain (residues 138–209). Thebackbone atoms of the residues 138–155,163–165 and 180–209 are superimposed.

17. Distribution of the electrostatic potential on the solvent-accessible surface of the central domain of XPA BLUE: C-terminalsubdomain positivepotential RED: zinc-ontaining subdomain negatively potential b, Mapping of the XPA residues with chemical shift perturbationor broadening effects in the (15N, 1H) HSQC spectra. The residues of which the amide resonances were perturbed upon complex formationwith 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 broadeningdefined by peak intensities decreased to <50 % of their original values) are indicated in magenta, and those of which the amide resonancesshowed specific broadening upon complex formation with RPA70181–422 (the peak intensities decreased to <65 % of their original values) are coloredgreen.

18. RPA

19. PDB ID: 1XPA

20. PDB ID: 1JMC

21. PDB ID: 1JMC Asymmetric Unit Ribbons Cylinders

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positivepotential, 印證其可能互相吸引而結合作用。

25. References

26. Nat. Struct. Biol. 5 1998 701–706. Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA Takahisa Ikegami1, Isao Kuraoka2, Masafumi Saijo2,Naohiko Kodo2, Yoshimasa Kyogoku3, KosukeMorikawa4, Kiyoji Tanaka2 and Masahiro Shirakawa1 1Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan. 2Institute for Molecular and Cellular Biology, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565, Japan. 3Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565, Japan. 4Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565, Japan.

27. Mutation Research 460 2000 257–275 Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA Kosuke Morikawa1, Masahiro Shirakawa2 1Department of Structural Biology, Biomolecular Engineering Research Institute BERI , 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan 2Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan

28. Biochemistry2005, 44, 971-978 MassSpectrometric 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.