Crystal structure of the SF3 helicase from adeno-associated virus type 2

Structure

Volumn 11, Issue 8, 2003, Pages 1025-1035

  James, J Anson ^a   Escalante, Carlos R ^a   Yoon Robarts, Miran ^a   Edwards, Thomas A ^a   Linden, R Michael ^a   Aggarwal, Aneel K ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; ARGININE; CELL PROTEIN; HELICASE; PROTEIN REP40; PROTEIN SUBUNIT; RECA PROTEIN; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; VIRUS ENZYME; VIRUS T ANTIGEN;

ADENOVIRUS 2; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; DNA DENATURATION; DNA INTEGRATION; DNA MODIFICATION; DNA PACKAGING; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME BINDING; ENZYME STRUCTURE; HYDROLYSIS; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MOTIF; SEQUENCE HOMOLOGY; SIMIAN VIRUS 40; STRUCTURAL HOMOLOGY; TRANSLATION REGULATION;

ADENO-ASSOCIATED VIRUS; ADENO-ASSOCIATED VIRUS 2; ADENOVIRIDAE; DNA VIRUSES; HUMAN ADENOVIRUS TYPE 2; SIMIAE; SIMIAN VIRUS 40;

EID: 0041630781     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(03)00152-7     Document Type: Article

References (57)

1. Bochtler M., Hartmann C., Song H.K., Bourenkov G.P., Bartunik H.D., Huber R. The structures of HslU and ATP-dependent protease HslU-HslIV. Nature. 403:2000;800-805.
2. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszeweski J., Nigles M., Punnu N.S.et al. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D54:1998;905-921.
3. Caruthers J.M., McKay D.B. Helicase structure and mechanism. Curr. Opin. Struct. Biol. 12:2002;123-133.
4. Chen G., Stenlund A. Characterization of the DNA-binding domain of the bovine papillomavirus replication initiator E1. J. Virol. 72:1998;2567-2576.
5. Christensen J., Cotmore S.F., Tattersall P. Minute virus of mice transcriptional activator protein NS1 binds directly to the transactivation region of the viral P38 promoter in a strictly ATP-dependent manner. J. Virol. 69:1995;5422-5430.
6. Cowtan, K. (1994). DM: an automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34-38.
7. + machines within the replisome Nat. Rev. Mol. Cell Biol. 3:2002;1-10.
8. Davis M.D., Wonderling R.S., Walker S.L., Owens R.A. Analysis of the effects of charge cluster mutations in adeno-associated virus Rep68 protein in vitro. J. Virol. 73:1999;2084-2093.
9. Dean F.B., Borowiec J.A., Eki T., Hurwitz J. The simian virus 40 T antigen double hexamer assembles around the DNA at the replication origin. J. Biol. Chem. 267:1992;14129-14137.
10. Dubielzig R., King J.A., Weger S., Kern A., Kleinschmidt J.A. Adeno-associated virus type 2 protein interactions. formation of pre-encapsidation complexes J. Virol. 73:1999;8989-8998.
11. Dutheil N., Shi F., Dupressoir T., Linden R.M. Adeno-associated virus site-specifically integrates into a muscle-specific DNA region. Proc. Natl. Acad. Sci. USA. 97:2000;4862-4866.
12. Erzberger J.P., Pirruccello M.M., Berger J.M. The structure of bacterial DnaA. implications for general mechanisms underlying DNA replication initiation EMBO J. 21:2002;4763-4773.
13. Fletcher R.J., Bishop B.E., Leon R.P., Sclafani R.A., Ogata C.M., Chen X.S. The structure and function of MCM from archael M. thermoautotrophicum. Nat. Struct. Biol. 10:2003;160-167.
14. Giraldo R. Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya. combined structural, functional and phylogenetic perspectives FEMS Microbiol. Rev. 26:2003;533-554.
15. Gorbalenya A.E., Koonin E.V. Helicases. amino acid sequence comparisons and structure-function relationships Curr. Opin. Struct. Biol. 3:1993;419-429.
16. + ATPase domain of RuvB motor protein is involved in the interaction with RuvA DNA recognition protein for branch migration of Holliday junctions. J. Biol. Chem. 276:2001;35024-35028.
17. Hartman J.J., Vale R.D. Microtubule disassembly by ATP-dependent oligomerization of the AAA enzyme katanin. Science. 286:1999;782-785.
18. Hendrickson W.A. Determination of macromolecular structures from anomalous diffraction of synchroton radiation. Science. 254:1991;51-58.
19. Hickman A.B., Ronning D.R., Kotin R.M., Dyda F. Structural unity among viral origin binding proteins. crystal structure of the nuclease domain of adeno-associated virus Rep Mol. Cell. 10:2002;327-337.
20. Im D.S., Muzyczka N. The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity. Cell. 61:1990;447-457.
21. Jones T., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A49:1991;1110-1119.
22. King J.A., Dubielzig R., Grimm D., Kleinschmidt J.A. DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids. EMBO J. 20:2001;3282-3291.
23. Koonin E.V. A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication. Nucleic Acids Res. 21:1993;2541-2547.
24. Kotin R.M., Siniscalco M., Samulski R.J., Zhu X.D., Hunter L., Laughlin C.A., McLaughlin S., Muzyczka N., Rocchi M., Berns K.I. Site-specific integration by adeno-associated virus. Proc. Natl. Acad. Sci. USA. 87:1990;2211-2215.
25. Laskowski R.A. Surfnet. a program for visualization molecular surfaces, cavities and intermolecular interactions J. Mol. Graph. 13:1995;323-330.
26. Lenzen C.U., Steinmann D., Whiteheart S.W., Weis W.I. Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein. Cell. 94:1998;525-536.
27. Linden R.M., Berns K.I. Molecular biology of adeno-associated viruses. Contrib. Microbiol. 4:2000;68-84.
28. Li D., Zhao R., Lilyestrom W., Gai D., Zhang R., DeCaprio J.A., Fanning E., Jochimiak A., Szakonyi G., Chen X.S. Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen. Nature. 423:2003;512-518.
29. Lohman T.M., Bjornson K.P. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65:1996;169-214.
30. Lupas A.N., Martin J. AAA proteins. Curr. Opin. Struct. Biol. 12:2002;746-753.
31. +. a class of chaperone-like atpases associated with the assembly, operation, and disassembly of protein complexes Genome Res. 9:1999;27-43.
32. Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.
33. Niedenzu T., Roleke D., Bains G., Scherzinger E., Saenger W. Crystal structure of the hexameric replicative helicase RepA of plasmid RSF1010. J. Mol. Biol. 306:2001;479-487.
34. + superfamily ATPases. common structure - diverse function Genes Cells. 6:2001;575-597.
35. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
36. Patel S., Latterich M. The AAA team. related ATPases with diverse functions Trends Cell Biol. 8:1998;65-71.
37. Putnam C.D., Clancy S.B., Tsuruta H., Gonzalez S., Wetmur J.G., Tainer J.A. Structure and mechanism of RuvB Holliday junction branch migration motor. J. Mol. Biol. 311:2001;297-310.
38. Samulski R.J., Zhu X., Xiao X., Brook J.D., Houssman D.E., Epstein N., Hunter L.A. Targeted integration of adeno-associated virus (AAV) into human chromosome 19. EMBO J. 10:1991;3941-3950.
39. Sawaya M.R., Guo S., Tabor S., Richardson C.C., Ellenberger T. Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7. Cell. 99:1999;167-177.
40. Singleton M.R., Sawaya M.R., Ellenberger T., Wigley D.B. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell. 101:2000;589-600.
41. Smith R.H., Kotin R.M. The Rep52 product of adeno-associated virus is a DNA helicase with 3′-to-5′ polarity. J. Virol. 72:1998;4874-4881.
42. Smith R.H., Spano A.J., Kotin R.M. The Rep78 gene product of adeno-associated virus self-associates to form a hexameric complex in the presence of AAV ori sequences. J. Virol. 71:1997;4461-4471.
43. Song H.K., Hartmann C., Ramachandran R., Bochtler M., Behrendt R., Moroder L., Huber R. Mutational studies of HslU and its docking mode with HslV. Proc. Natl. Acad. Sci. USA. 97:2000;14103-14108.
44. Sousa M.C., Trame C.B., Tsuruta S., Wilbanks S.M., Reddy R.S., McKay D. Crystal and solution structures of an HslVU protease-chaperone complex. Cell. 103:2000;633-643.
45. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55:1999;849-861.
46. Thompson J.D., Gibson T.J., Plewinak F., Jeanmougin F., Higgins D.G. The CLUSTAL-X interface. flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25:1997;4876-4882.
47. Tsaneva I.R., Muller B., West S.C. RuvA and RuvB proteins of Escherichia coli exhibit DNA helicase activity in vitro. Proc. Natl. Acad. Sci. USA. 90:1993;1315-1319.
48. Vale R.D. AAA proteins. lords of the ring J. Cell Biol. 150:2000;F13-F19.
49. Valle M., Gruss C., Halmer L., Carazo J.M., Donate L.E. Large T-antigen double hexamers imaged at the simian virus 40 origin of replication. Mol. Cell. Biol. 20:2000;34-41.
50. VanLoock M.S., Alexandrov A., Yu X., Cozzarelli N.R., Egelman E.H. SV40 large T antigen hexamer structure. domain organization and DNA-induced conformational changes Curr. Biol. 12:2002;472-476.
51. Walker S.L., Wonderling R.S., Owens R.A. Mutational analysis of the adeno-associated virus type 2 Rep68 protein helicase motifs. J. Virol. 71:1997;6996-7004.
52. Wang J., Song J.J., Franklin M.C., Kamtekar S., Im Y.J., Rho S.H., Seong I.S., Lee C.S., Chung C.H., Eom S.H. Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism. Structure. 9:2001;177-184. a.
53. Wang J., Song J.J., Seong I.S., Franklin M.C., Kamtekar S., Eom S.H., Chung C.H. Nucleotide-dependent conformational changes in a protease-associated ATPase HslU. Structure. 9:2001;1107-1116. b.
54. Yamada K., Kunishima N., Mayanagi K., Ohnishi T., Nishino T., Iwasaki H., Shinagawa H., Morikawa K. Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8. Proc. Natl. Acad. Sci. USA. 98:2001;1442-1447.
55. Yamada K., Miyata T., Tsuchiya D., Oyama T., Fujiwara Y., Ohnishi T., Iwasaki H., Shinagawa H., Ariyoshi M., Mayanagi K.et al. Crystal structure of the RuvA-RuvB complex. a structural basis for the Holliday junction migrating motor machinery Mol. Cell. 10:2002;671-681.
56. Yoon-Robarts M., Linden R.M. Identification of active site residues of the adeno-associated virus type 2 Rep endonuclease. J. Biol. Chem. 278:2003;4912-4918.
57. Yu R.C., Hanson P.I., Jahn R., Brunger A.T. Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP. Nat. Struct. Biol. 5:1998;803-811.