Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase

Journal of Molecular Biology

Volumn 284, Issue 4, 1998, Pages 1075-1081

  Chiu, Charles Y ^a   Cary, Robert B ^b   Chen, David J ^b   Peterson, Scott R ^b   Stewart, Phoebe L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Cryo electron microscopy; DNA dependent protein kinase; DNA PK; Double strand break repair; Image reconstruction

Indexed keywords

DNA; PROTEIN KINASE;

ARTICLE; CRYOELECTRON MICROSCOPY; ENZYME ACTIVE SITE; ENZYME STRUCTURE; HUMAN; HUMAN CELL; IMAGE ANALYSIS; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

MAMMALIA;

EID: 0032509097     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2212     Document Type: Article

References (35)

1. Adrian M., Dubochet J., Lepault J., McDowall A. W. Cryo-electron microscopy of viruses. Nature. 308:1984;32-36.
2. Anderson C. W., Lees-Miller S. P. The nuclear serine/threonine protein kinase DNA-PK. Crit. Rev. Eukaryot. Gene Expr. 2:1992;283-314.
3. Araki R., Fujimori A., Hamatani K., Mita K., Saito T., Mori M., Fukumura R., Morimyo M., Muto M., Itoh M., Tatsumi K., Abe M. Nonsense mutation at Tyr-4046 in the DNA-dependent protein kinase catalytic subunit of severe combined immune deficiency mice. Proc. Natl Acad. Sci. USA. 94:1997;2438-2443.
4. Berger J. M., Gamblin S. J., Harrison S. C., Wang J. C. Structure and mechanism of DNA topoisomerase II. Nature. 379:1996;225-232.
5. Biedermann K. A., Sun J. R., Giaccia A. J., Tosto L. M., Brown J. M. scid mutation in mice confers hypersensitivity to ionizing radiation and a deficiency in DNA double-strand break repair. Proc. Natl Acad. Sci. USA. 88:1991;1394-1397.
6. Blunt T., Gell D., Fox M., Taccioli G. E., Lehmann A. R., Jackson S. P., Jeggo P. A. Identification of a nonsense mutation in the carboxyl-terminal region of DNA-dependent protein kinase catalytic subunit in the scid mouse. Proc. Natl Acad. Sci. USA. 93:1996;10285-10290.
7. Böttcher B., Wynne S. A., Crowther R. A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 385:1997;88-91.
8. 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.
9. Chan D. W., Mody C. H., Ting N. S., Lees-Miller S. P. Purification and characterization of the double-stranded DNA-activated protein kinase, DNA-PK, from human placenta. Biochem. Cell Biol. 74:1996;67-73.
10. Conway J. F., Cheng N., Zlotnick A., Wingfield P. T., Stahl S. J., Steven A. C. Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature. 385:1997;91-94.
11. Danska J. S., Holland D. P., Mariathasan S., Williams K. M., Guidos C. J. Biochemical and genetic defects in the DNA-dependent protein kinase in murine scid lymphocytes. Mol. Cell. Biol. 16:1996;5507-5517.
12. Dube P., Bacher G., Stark H., Mueller F., Zemlin F., van Heel M., Brimacombe R. Correlation of the expansion segments in mammalian rRNA with the fine structure of the 80 S ribosome; a cryoelectron microscopic reconstruction of the rabbit reticulocyte ribosome at 21 Å resolution. J. Mol. Biol. 279:1998;403-421.
13. Dvir A., Peterson S. R., Knuth M. W., Lu H., Dynan W. S. Ku autoantigen is the regulatory component of a template-associated protein kinase that phosphorylates RNA polymerase II. Proc. Natl Acad. Sci. USA. 89:1992;11920-11924.
14. Dvir A., Stein L. Y., Calore B. L., Dynan W. S. Purification and characterization of a template-associated protein kinase that phosphorylates RNA polymerase II. J. Biol. Chem. 268:1993;10440-10447.
15. Fujimori A., Araki R., Fukumura R., Saito T., Mori M., Mita K., Tatsumi K., Abe M. The murine DNA-PKcs gene consists of 86 exons dispersed in more than 250 kb. Genomics. 45:1997;194-199.
16. Gottlieb T. M., Jackson S. P. The DNA-dependent protein kinase: requirement for DNA ends and association with Ku antigen. Cell. 72:1993;131-142.
17. Haley D. A., Horwitz J., Stewart P. L. The small heat-shock protein, alpha B-crystalline, has a variable quaternary structure. J. Mol. Biol. 277:1998;27-35.
18. 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.
19. Hartley K. O., Gell D., Smith G. C., Zhang H., Divecha N., Connelly M. A., Admon A., Lees-Miller S. P., Anderson C. W., Jackson S. P. DNA-dependent protein kinase catalytic subunit: a relative of phosphatidylinositol 3-kinase and the ataxia telangiectasia gene product. Cell. 82:1995;849-856.
20. Hendrickson E. A., Qin X. Q., Bump E. A., Schatz D. G., Oettinger M., Weaver D. T. A link between double-strand break-related repair and V(D)J recombination: the scid mutation. Proc. Natl Acad. Sci. USA. 88:1991;4061-4065.
21. Jeggo P. A., Taccioli G. E., Jackson S. P. Menage a trois: double strand break repair, V(D)J recombination and DNA-PK. Bioessays. 17:1995;949-957.
22. Jin S., Kharbanda S., Haver B., Kuge D., Weaver D. T. Binding of Ku and c-Abl at the kinase homology region of DNA-dependent protein kinase catalytic subunit. J. Biol. Chem. 272:1997;24763-24766.
23. Kelman Z. PCNA: structure, functions and interactions. Oncogene. 14:1997;629-640.
24. Kong X. P., Onrust R., O'Donnell M., Kuriyan J. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell. 69:1992;425-437.
25. Krishna T. S., Kong X. P., Gary S., Burgers P. M., Kuriyan J. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell. 79:1994;1233-1243.
26. Malhotra A., Penczek P., Agrawal R. K., Gabashvili I. S., Grassucci R. A., Junemann R., Burkhardt N., Nierhaus K. H., Frank J. Escherichia coli 70 S ribosome at 15 Å resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein. J. Mol. Biol. 280:1998;103-116.
27. Peterson S. R., Kurimasa A., Oshimura M., Dynan W. S., Bradbury E. M., Chen D. J. Loss of the catalytic subunit of the DNA-dependent protein kinase in DNA double-strand-break-repair mutant mammalian cells. Proc. Natl Acad. Sci. USA. 92:1995;3171-3174.
28. Ramsden D. A., Gellert M. Ku protein stimulates DNA end joining by mammalian DNA ligases: a direct role for Ku in repair of DNA double-strand breaks. EMBO J. 17:1998;609-614.
29. Redinbo M. R., Stewart L., Kuhn P., Champoux J. J., Hol W. G. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science. 279:1998;1504-1513.
30. Roseman A. M., Chen S., White H., Braig K., Saibil H. R. The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell. 87:1996;241-251.
31. Shah A. K., Stewart P. L. QVIEW: Software for rapid selection of particles from digital electron micrographs. J. Struct. Biol. 123:1998;17-21.
32. Sinden R. R. DNA Structure and Function. 1994;Academic Press, San Diego.
33. Stewart P. L., Fuller S. D., Burnett R. M. Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO J. 12:1993;2589-2599.
34. van Heel M., Harauz G., Orlova E. V., Schmidt R., Schatz M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116:1996;17-24.
35. Yaneva M., Kowalewski T., Lieber M. R. Interaction of DNA-dependent protein kinase with DNA and with Ku: biochemical and atomic-force microscopy studies. EMBO J. 16:1997;5098-5112.