The Archaeal XPB Protein is a ssDNA-Dependent ATPase with a Novel Partner

Journal of Molecular Biology

Volumn 376, Issue 3, 2008, Pages 634-644

  Richards, Jodi D ^a   Cubeddu, Liza ^a   Roberts, Jennifer ^a   Liu, Huanting ^a   White, Malcolm F ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

archaea; DNA repair; helicase; transcription; XPB

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ARCHAEAL PROTEIN; BACTERIAL PROTEIN; BAX1 PROTEIN; GENE PRODUCT; HELICASE; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; XPB PROTEIN;

ARTICLE; BINDING AFFINITY; DNA REPAIR; DNA TRANSCRIPTION; ENZYME ACTIVITY; GENE INTERACTION; GENE SWITCHING; GENETIC TRANSCRIPTION; GENOME; MOLECULAR PROBE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; SULFOLOBUS SOLFATARICUS;

ARCHAEA; CRENARCHAEOTA; EUKARYOTA; SULFOLOBUS SOLFATARICUS;

EID: 38649138320     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.12.019     Document Type: Article

References (40)

1. Laine J.P., Mocquet V., and Egly J.M. TFIIH enzymatic activities in transcription and nucleotide excision repair. Methods Enzymol. 408 (2006) 246-263
2. Coin F., Bergmann E., Tremeau-Bravard A., and Egly J.M. Mutations in XPB and XPD helicases found in xeroderma pigmentosum patients impair the transcription function of TFIIH. EMBO J. 18 (1999) 1357-1366
3. Winkler G.S., Araujo S.J., Fiedler U., Vermeulen W., Coin F., Egly J.M., et al. TFIIH with inactive XPD helicase functions in transcription initiation but is defective in DNA repair. J. Biol. Chem. 275 (2000) 4258-4266
4. Coin F., Oksenych V., and Egly J.M. Distinct roles for the XPB/p52 and XPD/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair. Mol. Cell 26 (2007) 245-256
5. Coin F., Marinoni J.C., and Egly J.M. Mutations in XPD helicase prevent its interaction and regulation by p44, another subunit of TFIIH, resulting in xeroderma pigmentosum (XP) and trichothiodystrophy (TTD) phenotypes. Pathol. Biol. (Paris) 46 (1998) 679-680
6. Lin Y.C., Choi W.S., and Gralla J.D. TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape. Nat. Struct. Mol. Biol. 12 (2005) 603-607
7. Miller G., and Hahn S. A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex. Nat. Struct. Mol. Biol. 13 (2006) 603-610
8. Kelman Z., and White M.F. Archaeal DNA replication and repair. Curr. Opin. Microbiol. 8 (2005) 669-676
9. Bell S.D., and Jackson S.P. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6 (1998) 222-228
10. Wadsworth R.I., and White M.F. Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res. 29 (2001) 914-920
11. Chedin F., Seitz E.M., and Kowalczykowski S.C. Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins. Trends Biochem. Sci. 23 (1998) 273-277
12. Roberts J.A., Bell S.D., and White M.F. An archaeal XPF repair endonuclease dependent on a heterotrimeric PCNA. Mol. Microbiol. 48 (2003) 361-371
13. Komori K., Fujikane R., Shinagawa H., and Ishino Y. Novel endonuclease in Archaea cleaving DNA with various branched structure. Genes Genet. Syst. 77 (2002) 227-241
14. Grogan D.W. The question of DNA repair in hyperthermophilic archaea. Trends Microbiol. 8 (2000) 180-185
15. White M.F. DNA repair. In: Garrett R.A., and Klenk H.P. (Eds). Archaea: Evolution, Physiology and Molecular Biology (2007), Blackwell Publishing Ltd., Oxford 171-184
16. Fan L., Arvai A.S., Cooper P.K., Iwai S., Hanaoka F., and Tainer J.A. Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Mol. Cell 22 (2006) 27-37
17. She Q., Singh R.K., Confalonieri F., Zivanovic Y., Allard G., Awayez M.J., et al. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl Acad. Sci. USA 98 (2001) 7835-7840
18. Dillingham M.S., Soultanas P., Wiley P., Webb M.R., and Wigley D.B. Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase. Proc. Natl Acad. Sci. USA 98 (2001) 8381-8387
19. Voloshin O.N., and Camerini-Otero R.D. The DinG protein from Escherichia coli is a structure-specific helicase. J. Biol. Chem. 282 (2007) 18437-18447
20. Singleton M.R., Dillingham M.S., and Wigley D.B. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76 (2007) 23-50
21. Rudolf J., Makrantoni V., Ingledew W.J., Stark M.J., and White M.F. The DNA repair helicases XPD and FancJ have essential iron-sulfur domains. Mol. Cell 23 (2006) 801-808
22. Richards J.D., Johnson K.A., Liu H., McRobbie A.-M., McMahon S.A., Oke M., et al. Structure of the DNA repair helicase HEL308 reveals DNA binding and autoinhibitory domains. J. Biol. Chem. (2007) 10.1074/jbc.M707548200 in press
23. Morris P.D., Tackett A.J., and Raney K.D. Biotin-streptavidin-labeled oligonucleotides as probes of helicase mechanisms. Methods 23 (2001) 149-159
24. Morris P.D., and Raney K.D. DNA helicases displace streptavidin from biotin-labeled oligonucleotides. Biochemistry 38 (1999) 5164-5171
25. T difference" formula. J. Mol. Med. 84 (2006) 901-910
26. Cubeddu L., and White M.F. DNA damage detection by an archaeal single-stranded DNA-binding protein. J. Mol. Biol. 353 (2005) 507-516
27. White M.F. Archaeal DNA repair: paradigms and puzzles. Biochem. Soc. Trans. 31 (2003) 690-693
28. Kinch L.N., Ginalski K., Rychlewski L., and Grishin N.V. Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Nucleic Acids Res. 33 (2005) 3598-3605
29. Chen L., Brugger K., Skovgaard M., Redder P., She Q., Torarinsson E., et al. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J. Bacteriol. 187 (2005) 4992-4999
30. Guzder S.N., Sung P., Bailly V., Prakash L., and Prakash S. RAD25 is a DNA helicase required for DNA repair and RNA polymerase II transcription. Nature 369 (1994) 578-581
31. Ma H., and Zou Y. Thermodynamic characterization of the interaction of mutant UvrB protein with damaged DNA. Biochemistry 43 (2004) 4206-42011
32. Iakoucheva L.M., Walker R.K., van Houten B., and Ackerman E.J. Equilibrium and stop-flow kinetic studies of fluorescently labeled DNA substrates with DNA repair proteins XPA and replication protein A. Biochemistry 41 (2002) 131-143
33. Seroz T., Perez C., Bergmann E., Bradsher J., and Egly J.M. p44/SSL1, the regulatory subunit of the XPD/RAD3 helicase, plays a crucial role in the transcriptional activity of TFIIH. J. Biol. Chem. 275 (2000) 33260-33266
34. Jawhari A., Laine J.P., Dubaele S., Lamour V., Poterszman A., Coin F., et al. p52 mediates XPB function within the transcription/repair factor TFIIH. J. Biol. Chem. 277 (2002) 31761-31767
35. Lin Y.C., and Gralla J.D. Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE. Nucleic Acids Res. 33 (2005) 3072-3081
36. Shen L.N., Dong C., Liu H., Naismith J.H., and Hay R.T. The structure of SENP1-SUMO-2 complex suggests a structural basis for discrimination between SUMO paralogues during processing. Biochem. J. 397 (2006) 279-288
37. Seetharamappa J., Oke M., Liu H., McMahon S.A., Johnson K.A., Carter L., et al. Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5′-phosphate-dependent aminotransferase. Acta Crystallogr. Sect. F 63 (2007) 452-456
38. Studier F.W. Protein production by auto-induction in high density shaking cultures. Protein Expression Purif. 41 (2005) 207-234
39. Dorazi R., Gotz D., Munro S., Bernander R., and White M.F. Equal rates of repair of DNA photoproducts in transcribed and non-transcribed strands in Sulfolobus solfataricus. Mol. Microbiol. 63 (2007) 521-529
40. Roberts J., and White M.F. An archaeal endonuclease displays key properties of both eukaryal XPF-ERCC1 and Mus81. J. Biol. Chem. 280 (2005) 5924-5928