Solution structure of the C-terminal domain of Ku80 suggests important sites for protein-protein interactions

Structure

Volumn 12, Issue 3, 2004, Pages 495-502

  Zhang, Ziming ^a   Hu, Weidong ^a   Cano, Leticia ^a   Lee, Terry D ^a   Chen, David J ^b   Chen, Yuan ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DIMER; KU ANTIGEN; PROTEIN KU80; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL FUNCTION; GENETIC TRANSCRIPTION; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; TELOMERE;

ALKYL AND ARYL TRANSFERASES; AMINO ACID SEQUENCE; ANIMALS; ANTIGENS, NUCLEAR; CRICETINAE; DNA-BINDING PROTEINS; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; MICE; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RATS; SEQUENCE ALIGNMENT;

EID: 1542581549     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.02.007     Document Type: Article

References (33)

1. Andrade M.A., Perez-Iratxeta C., Ponting C.P. Protein repeats. structures, functions, and evolution J. Struct. Biol. 134:2001;117-131. a.
2. Andrade M.A., Petosa C., O'Donoghue S.I., Muller C.W., Bork P. Comparison of ARM and HEAT protein repeats. J. Mol. Biol. 309:2001;1-18. b.
3. Bailey S.M., Meyne J., Chen D.J., Kurimasa A., Li G.C., Lehnert B.E., Goodwin E.H. DNA double-strand break repair proteins are required to cap the ends of mammalian chromosomes. Proc. Natl. Acad. Sci. USA. 96:1999;14899-14904.
4. Bax A., Vuister G.W., Grzesiek S., Delaglio F., Wang A.C., Tschudin R., Zhu G. Measurement of homo- and heteronuclear J couplings from quantitative J correlation. Methods Enzymol. 239:1994;79-105.
5. Cary R.B., Peterson S.R., Wang J., Bear D.G., Bradbury E.M., Chen D.J. DNA looping by Ku and the DNA-dependent protein kinase. Proc. Natl. Acad. Sci. USA. 94:1997;4267-4272.
6. Chook Y.M., Blobel G. Structure of the nuclear transport complex karyopherin-beta2-Ran x GppNHp. Nature. 399:1999;230-237.
7. Clore G.M., Gronenborn A.M. Multidimensional heteronuclear nuclear magnetic resonance of proteins. Methods Enzymol. 239:1994;349-363.
8. Clore G.M., Bax A., Gronenborn A.M. Stereospecific assignment of beta-methylene protons in larger proteins using 3D 15N-separated Hartmann-Hahn and 13C-separated rotating frame Overhauser spectroscopy. J. Biomol. NMR. 1:1991;13-22.
9. Collins B.M., McCoy A.J., Kent H.M., Evans P.R., Owen D.J. Molecular architecture and functional model of the endocytic AP2 complex. Cell. 109:2002;523-535.
10. Critchlow S.E., Bowater R.P., Jackson S.P. Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV. Curr. Biol. 7:1997;588-598.
11. Farrow N.A., Muhandiram R., Singer A.U., Pascal S.M., Kay C.M., Gish G., Shoelson S.E., Pawson T., Forman-Kay J.D., Kay L.E. Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry. 33:1994;5984-6003.
12. Gell D., Jackson S.P. Mapping of protein-protein interactions within the DNA-dependent protein kinase complex. Nucleic Acids Res. 27:1999;3494-3502.
13. Guntert P., Mumenthaler C., Wuthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273:1997;283-298.
14. Hammarsten O., Chu G. DNA-dependent protein kinase. DNA binding and activation in the absence of Ku Proc. Natl. Acad. Sci. USA. 95:1998;525-530.
15. Holm L., Sander C. Dali. a network tool for protein structure comparison Trends Biochem. Sci. 20:1995;478-480.
16. Hsu H.L., Gilley D., Blackburn E.H., Chen D.J. Ku is associated with the telomere in mammals. Proc. Natl. Acad. Sci. USA. 96:1999;12454-12458.
17. Hsu H.L., Yannone S.M., Chen D.J. Defining interactions between DNA-PK and ligase IV/XRCC4. DNA Repair (Amst.). 1:2002;225-235.
18. Karmakar P., Snowden C.M., Ramsden D.A., Bohr V.A. Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus. Nucleic Acids Res. 30:2002;3583-3591.
19. Kuboniwa H., Grzesiek S., Delaglio F., Bax A. Measurement of HN-H alpha J couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods. J. Biomol. NMR. 4:1994;871-878.
20. Kurimasa A., Kumano S., Boubnov N.V., Story M.D., Tung C.S., Peterson S.R., Chen D.J. Requirement for the kinase activity of human DNA-dependent protein kinase catalytic subunit in DNA strand break rejoining. Mol. Cell. Biol. 19:1999;3877-3884.
21. Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., Thornton J.M. Aqua and procheck-nmr. programs for checking the quality of protein structures solved by nmr J. Biomol. NMR. 8:1996;477-486.
22. Linge J.P., Habeck M., Rieping W., Nilges M. Aria. automated noe assignment and nmr structure calculation Bioinformatics. 19:2003;315-316.
23. Ludwig D.L., Chen F., Peterson S.R., Nussenzweig A., Li G.C., Chen D.J. Ku80 gene expression is Sp1-dependent and sensitive to CpG methylation within a novel cis element. Gene. 199:1997;181-194.
24. Mahajan K.N., Nick McElhinny S.A., Mitchell B.S., Ramsden D.A. Association of DNA polymerase mu (pol mu) with Ku and ligase IV. role for pol mu in end-joining double-strand break repair Mol. Cell. Biol. 22:2002;5194-5202.
25. Martin S.G., Laroche T., Suka N., Grunstein M., Gasser S.M. Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell. 97:1999;621-633.
26. Rost B. Phd. predicting one-dimensional protein structure by profile-based neural networks Methods Enzymol. 266:1996;525-539.
27. Sawada M., Sun W., Hayes P., Leskov K., Boothman D.A., Matsuyama S. Ku70 suppresses the apoptotic translocation of Bax to mitochondria. Nat. Cell Biol. 5:2003;320-329.
28. Schild-Poulter C., Pope L., Giffin W., Kochan J.C., Ngsee J.K., Traykova-Andonova M., Hache R.J. The binding of Ku antigen to homeodomain proteins promotes their phosphorylation by DNA-dependent protein kinase. J. Biol. Chem. 276:2001;16848-16856.
29. Singleton B.K., Torres-Arzayus M.I., Rottinghaus S.T., Taccioli G.E., Jeggo P.A. The C terminus of Ku80 activates the DNA-dependent protein kinase catalytic subunit. Mol. Cell. Biol. 19:1999;3267-3277.
30. Walker J.R., Corpina R.A., Goldberg J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature. 412:2001;607-614.
31. Willis D.M., Loewy A.P., Charlton-Kachigian N., Shao J.S., Ornitz D.M., Towler D.A. Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex. J. Biol. Chem. 277:2002;37280-37291.
32. Zhang H., Seabra M.C., Deisenhofer J. Crystal structure of Rab geranylgeranyltransferase at 2.0 A resolution. Struct. Fold. Des. 8:2000;241-251.
33. Zhang Z., Zhu L., Lin D., Chen F., Chen D.J., Chen Y. The three-dimensional structure of the C-terminal DNA-binding domain of human Ku70. J. Biol. Chem. 276:2001;38231-38236.