Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/24014
標題: 細菌第IIA型 DNA 拓撲異構酵素 C 端區域之晶體結構研究
Crystallographic Studies of the C-terminal Domains of the Bacterial Type IIA DNA Topoisomerases
作者: 謝東儒
Hsieh, Tung-Ju
關鍵字: Type IIA DNA topoisomerases: DNA TopoIIAs
第IIA型DNA 拓撲異構酵素
出版社: 生物化學研究所
引用: References 1. Watson, J.D. and Crick, F.H. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171, 737-738. 2. Travers, A. and Muskhelishvili, G. (2005) Bacterial chromatin. Curr Opin Genet Dev, 15, 507-514. 3. Luijsterburg, M.S., Noom, M.C., Wuite, G.J. and Dame, R.T. (2006) The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J Struct Biol, 156, 262-272. 4. Wang, J.C. (1996) DNA topoisomerases. Annu Rev Biochem, 65, 635-692. 5. Postow, L., Crisona, N.J., Peter, B.J., Hardy, C.D. and Cozzarelli, N.R. (2001) Topological challenges to DNA replication: conformations at the fork. Proc Natl Acad Sci U S A, 98, 8219-8226. 6. Espeli, O. and Marians, K.J. (2004) Untangling intracellular DNA topology. Mol Microbiol, 52, 925-931. 7. Wang, J.C. (2002) Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol, 3, 430-440. 8. Champoux, J.J. (2001) DNA topoisomerases: structure, function, and mechanism. Annu Rev Biochem, 70, 369-413. 9. Zechiedrich, E.L., Khodursky, A.B., Bachellier, S., Schneider, R., Chen, D., Lilley, D.M. and Cozzarelli, N.R. (2000) Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J Biol Chem, 275, 8103-8113. 10. Wang, J.C. (1979) Helical repeat of DNA in solution. Proc Natl Acad Sci U S A, 76, 200-203. 11. Charvin, G., Bensimon, D. and Croquette, V. (2003) Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases. Proc Natl Acad Sci U S A, 100, 9820-9825. 12. Hande, K.R. (1998) Etoposide: four decades of development of a topoisomerase II inhibitor. Eur J Cancer, 34, 1514-1521. 13. Walker, J.V. and Nitiss, J.L. (2002) DNA topoisomerase II as a target for cancer chemotherapy. Cancer Invest, 20, 570-589. 14. Baldwin, E.L. and Osheroff, N. (2005) Etoposide, topoisomerase II and cancer. Curr Med Chem Anticancer Agents, 5, 363-372. 15. Hande, K.R. (1998) Clinical applications of anticancer drugs targeted to topoisomerase II. Biochim Biophys Acta, 1400, 173-184. 16. Pommier, Y. and Marchand, C. (2005) Interfacial inhibitors of protein-nucleic acid interactions. Curr Med Chem Anticancer Agents, 5, 421-429. 17. Fortune, J.M. and Osheroff, N. (2000) Topoisomerase II as a target for anticancer drugs: when enzymes stop being nice. Prog Nucleic Acid Res Mol Biol, 64, 221-253. 18. Wilstermann, A.M. and Osheroff, N. (2003) Stabilization of eukaryotic topoisomerase II-DNA cleavage complexes. Curr Top Med Chem, 3, 321-338. 19. Li, T.K. and Liu, L.F. (2001) Tumor cell death induced by topoisomerase-targeting drugs. Annu Rev Pharmacol Toxicol, 41, 53-77. 20. Kaufmann, S.H. (1998) Cell death induced by topoisomerase-targeted drugs: more questions than answers. Biochim Biophys Acta, 1400, 195-211. 21. Tse, Y.C., Kirkegaard, K. and Wang, J.C. (1980) Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA. J Biol Chem, 255, 5560-5565. 22. Depew, R.E., Liu, L.F. and Wang, J.C. (1978) Interaction between DNA and Escherichia coli protein omega. Formation of a complex between single-stranded DNA and omega protein. J Biol Chem, 253, 511-518. 23. Liu, L.F. and Wang, J.C. (1979) Interaction between DNA and Escherichia coli DNA topoisomerase I. Formation of complexes between the protein and superhelical and nonsuperhelical duplex DNAs. J Biol Chem, 254, 11082-11088. 24. Champoux, J.J. (1981) DNA is linked to the rat liver DNA nicking-closing enzyme by a phosphodiester bond to tyrosine. J Biol Chem, 256, 4805-4809. 25. Liu, L.F., Rowe, T.C., Yang, L., Tewey, K.M. and Chen, G.L. (1983) Cleavage of DNA by mammalian DNA topoisomerase II. J Biol Chem, 258, 15365-15370. 26. Brown, P.O. and Cozzarelli, N.R. (1979) A sign inversion mechanism for enzymatic supercoiling of DNA. Science, 206, 1081-1083. 27. Morrison, A. and Cozzarelli, N.R. (1979) Site-specific cleavage of DNA by E. coli DNA gyrase. Cell, 17, 175-184. 28. Sander, M. and Hsieh, T. (1983) Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. J Biol Chem, 258, 8421-8428. 29. Forterre, P., Gribaldo, S., Gadelle, D. and Serre, M.C. (2007) Origin and evolution of DNA topoisomerases. Biochimie, 89, 427-446. 30. Schoeffler, A.J. and Berger, J.M. (2008) DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q Rev Biophys, 41, 41-101. 31. Wang, J.C. (1998) Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Q Rev Biophys, 31, 107-144. 32. Bellon, S., Parsons, J.D., Wei, Y., Hayakawa, K., Swenson, L.L., Charifson, P.S., Lippke, J.A., Aldape, R. and Gross, C.H. (2004) Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase. Antimicrob Agents Chemother, 48, 1856-1864. 33. Wigley, D.B., Davies, G.J., Dodson, E.J., Maxwell, A. and Dodson, G. (1991) Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature, 351, 624-629. 34. Classen, S., Olland, S. and Berger, J.M. (2003) Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proc Natl Acad Sci U S A, 100, 10629-10634. 35. Corbett, K.D. and Berger, J.M. (2003) Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution. EMBO J, 22, 151-163. 36. Dutta, R. and Inouye, M. (2000) GHKL, an emergent ATPase/kinase superfamily. Trends Biochem Sci, 25, 24-28. 37. Bjergbaek, L., Kingma, P., Nielsen, I.S., Wang, Y., Westergaard, O., Osheroff, N. and Andersen, A.H. (2000) Communication between the ATPase and cleavage/religation domains of human topoisomerase IIalpha. J Biol Chem, 275, 13041-13048. 38. Aravind, L., Leipe, D.D. and Koonin, E.V. (1998) Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res, 26, 4205-4213. 39. Lima, C.D., Wang, J.C. and Mondragon, A. (1994) Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature, 367, 138-146. 40. Liu, Q. and Wang, J.C. (1999) Similarity in the catalysis of DNA breakage and rejoining by type IA and IIA DNA topoisomerases. Proc Natl Acad Sci U S A, 96, 881-886. 41. Noble, C.G. and Maxwell, A. (2002) The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J Mol Biol, 318, 361-371. 42. Osheroff, N. (1987) Role of the divalent cation in topoisomerase II mediated reactions. Biochemistry, 26, 6402-6406. 43. West, K.L., Meczes, E.L., Thorn, R., Turnbull, R.M., Marshall, R. and Austin, C.A. (2000) Mutagenesis of E477 or K505 in the B'' domain of human topoisomerase II beta increases the requirement for magnesium ions during strand passage. Biochemistry, 39, 1223-1233. 44. Zhu, C.X. and Tse-Dinh, Y.C. (2000) The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change. J Biol Chem, 275, 5318-5322. 45. McKay, D.B. and Steitz, T.A. (1981) Structure of catabolite gene activator protein at 2.9 A resolution suggests binding to left-handed B-DNA. Nature, 290, 744-749. 46. Harrison, S.C. and Aggarwal, A.K. (1990) DNA recognition by proteins with the helix-turn-helix motif. Annu Rev Biochem, 59, 933-969. 47. Berger, J.M., Gamblin, S.J., Harrison, S.C. and Wang, J.C. (1996) Structure and mechanism of DNA topoisomerase II. Nature, 379, 225-232. 48. Gajiwala, K.S. and Burley, S.K. (2000) Winged helix proteins. Curr Opin Struct Biol, 10, 110-116. 49. Morais Cabral, J.H., Jackson, A.P., Smith, C.V., Shikotra, N., Maxwell, A. and Liddington, R.C. (1997) Crystal structure of the breakage-reunion domain of DNA gyrase. Nature, 388, 903-906. 50. Fass, D., Bogden, C.E. and Berger, J.M. (1999) Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands. Nat Struct Biol, 6, 322-326. 51. McClendon, A.K., Dickey, J.S. and Osheroff, N. (2006) Ability of viral topoisomerase II to discern the handedness of supercoiled DNA: bimodal recognition of DNA geometry by type II enzymes. Biochemistry, 45, 11674-11680. 52. Corbett, K.D., Shultzaberger, R.K. and Berger, J.M. (2004) The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc Natl Acad Sci U S A, 101, 7293-7298. 53. Hsieh, T.J., Farh, L., Huang, W.M. and Chan, N.L. (2004) Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis. J Biol Chem, 279, 55587-55593. 54. Corbett, K.D., Schoeffler, A.J., Thomsen, N.D. and Berger, J.M. (2005) The structural basis for substrate specificity in DNA topoisomerase IV. J Mol Biol, 351, 545-561. 55. McClendon, A.K. and Osheroff, N. (2006) The geometry of DNA supercoils modulates topoisomerase-mediated DNA cleavage and enzyme response to anticancer drugs. Biochemistry, 45, 3040-3050. 56. Roca, J. and Wang, J.C. (1994) DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism. Cell, 77, 609-616. 57. Harkins, T.T., Lewis, T.J. and Lindsley, J.E. (1998) Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 2. Kinetic mechanism for the sequential hydrolysis of two ATP. Biochemistry, 37, 7299-7312. 58. Baird, C.L., Harkins, T.T., Morris, S.K. and Lindsley, J.E. (1999) Topoisomerase II drives DNA transport by hydrolyzing one ATP. Proc Natl Acad Sci U S A, 96, 13685-13690. 59. Dong, K.C. and Berger, J.M. (2007) Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature, 450, 1201-1205. 60. Gellert, M., Mizuuchi, K., O''Dea, M.H. and Nash, H.A. (1976) DNA gyrase: an enzyme that introduces superhelical turns into DNA. Proc Natl Acad Sci U S A, 73, 3872-3876. 61. Kato, J., Nishimura, Y., Imamura, R., Niki, H., Hiraga, S. and Suzuki, H. (1990) New topoisomerase essential for chromosome segregation in E. coli. Cell, 63, 393-404. 62. Adams, D.E., Shekhtman, E.M., Zechiedrich, E.L., Schmid, M.B. and Cozzarelli, N.R. (1992) The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell, 71, 277-288. 63. Zechiedrich, E.L. and Cozzarelli, N.R. (1995) Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev, 9, 2859-2869. 64. Funnell, B.E., Baker, T.A. and Kornberg, A. (1987) In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. J Biol Chem, 262, 10327-10334. 65. Miller, W.G. and Simons, R.W. (1993) Chromosomal supercoiling in Escherichia coli. Mol Microbiol, 10, 675-684. 66. Khodursky, A.B., Peter, B.J., Schmid, M.B., DeRisi, J., Botstein, D., Brown, P.O. and Cozzarelli, N.R. (2000) Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc Natl Acad Sci U S A, 97, 9419-9424. 67. Hiasa, H. and Marians, K.J. (1996) Two distinct modes of strand unlinking during theta-type DNA replication. J Biol Chem, 271, 21529-21535. 68. Khodursky, A.B., Zechiedrich, E.L. and Cozzarelli, N.R. (1995) Topoisomerase IV is a target of quinolones in Escherichia coli. Proc Natl Acad Sci U S A, 92, 11801-11805. 69. Kato, J., Suzuki, H. and Ikeda, H. (1992) Purification and characterization of DNA topoisomerase IV in Escherichia coli. J Biol Chem, 267, 25676-25684. 70. Crisona, N.J., Strick, T.R., Bensimon, D., Croquette, V. and Cozzarelli, N.R. (2000) Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev, 14, 2881-2892. 71. Stone, M.D., Bryant, Z., Crisona, N.J., Smith, S.B., Vologodskii, A., Bustamante, C. and Cozzarelli, N.R. (2003) Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc Natl Acad Sci U S A, 100, 8654-8659. 72. Gadelle, D., Filee, J., Buhler, C. and Forterre, P. (2003) Phylogenomics of type II DNA topoisomerases. Bioessays, 25, 232-242. 73. Shiozaki, K. and Yanagida, M. (1991) A functional 125-kDa core polypeptide of fission yeast DNA topoisomerase II. Mol Cell Biol, 11, 6093-6102. 74. Crenshaw, D.G. and Hsieh, T. (1993) Function of the hydrophilic carboxyl terminus of type II DNA topoisomerase from Drosophila melanogaster. II. In vivo studies. J Biol Chem, 268, 21335-21343. 75. Caron, P.R., Watt, P. and Wang, J.C. (1994) The C-terminal domain of Saccharomyces cerevisiae DNA topoisomerase II. Mol Cell Biol, 14, 3197-3207. 76. Adachi, N., Miyaike, M., Kato, S., Kanamaru, R., Koyama, H. and Kikuchi, A. (1997) Cellular distribution of mammalian DNA topoisomerase II is determined by its catalytically dispensable C-terminal domain. Nucleic Acids Res, 25, 3135-3142. 77. Qi, Y., Pei, J. and Grishin, N.V. (2002) C-terminal domain of gyrase A is predicted to have a beta-propeller structure. Proteins, 47, 258-264. 78. Kampranis, S.C. and Maxwell, A. (1996) Conversion of DNA gyrase into a conventional type II topoisomerase. Proc Natl Acad Sci U S A, 93, 14416-14421. 79. Peng, H. and Marians, K.J. (1995) The interaction of Escherichia coli topoisomerase IV with DNA. J Biol Chem, 270, 25286-25290. 80. Liu, L.F. and Wang, J.C. (1978) DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell, 15, 979-984. 81. Reece, R.J. and Maxwell, A. (1991) The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Nucleic Acids Res, 19, 1399-1405. 82. Knight, S.W. and Samuels, D.S. (1999) Natural synthesis of a DNA-binding protein from the C-terminal domain of DNA gyrase A in Borrelia burgdorferi. EMBO J, 18, 4875-4881. 83. Kampranis, S.C., Bates, A.D. and Maxwell, A. (1999) A model for the mechanism of strand passage by DNA gyrase. Proc Natl Acad Sci U S A, 96, 8414-8419. 84. Kirchhausen, T., Wang, J.C. and Harrison, S.C. (1985) DNA gyrase and its complexes with DNA: direct observation by electron microscopy. Cell, 41, 933-943. 85. Ward, D. and Newton, A. (1997) Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus. Mol Microbiol, 26, 897-910. 86. Ramakrishnan, V., Finch, J.T., Graziano, V., Lee, P.L. and Sweet, R.M. (1993) Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature, 362, 219-223. 87. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol, 276, 307-326. 88. Collaborative Computational Project, N. (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr, 50, 760-763. 89. Weeks, C.M. and Miller, R. (1999) Optimizing Shake-and-Bake for proteins. Acta Crystallogr D Biol Crystallogr, 55, 492-500. 90. Fortelle, E.d.l. and Bricogne, G. (1997) Maximum-Likelihood Heavy-Atom Parameter Refinement for Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods. Methods Enzymol, 276, 472-494. 91. Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A, 47 ( Pt 2), 110-119. 92. Collaborative Computational Project, N. (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallog sect D, 764-767. 93. Jawad, Z. and Paoli, M. (2002) Novel sequences propel familiar folds. Structure, 10, 447-454. 94. Paoli, M. (2001) Protein folds propelled by diversity. Prog Biophys Mol Biol, 76, 103-130. 95. Fulop, V. and Jones, D.T. (1999) Beta propellers: structural rigidity and functional diversity. Curr Opin Struct Biol, 9, 715-721. 96. Engel, M., Hoffmann, T., Wagner, L., Wermann, M., Heiser, U., Kiefersauer, R., Huber, R., Bode, W., Demuth, H.U. and Brandstetter, H. (2003) The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism. Proc Natl Acad Sci U S A, 100, 5063-5068. 97. Hutchinson, E.G. and Thornton, J.M. (1994) A revised set of potentials for beta-turn formation in proteins. Protein Sci, 3, 2207-2216. 98. Nelson, D.L. and Cox, M.M. (2004), Lehninger PRINCIPLES OF BIOCHEMISTRY, pp. 123-125. 99. Malkov, S., Zivkovic, M.V., Beljanski, M.V. and Zaric, S.D. (2005) Correlations of amino acids with secondary structure types: connection with amino acid structure. 100. Kang, S., Han, J.S., Park, J.H., Skarstad, K. and Hwang, D.S. (2003) SeqA protein stimulates the relaxing and decatenating activities of topoisomerase IV. J Biol Chem, 278, 48779-48785. 101. Espeli, O., Lee, C. and Marians, K.J. (2003) A physical and functional interaction between Escherichia coli FtsK and topoisomerase IV. J Biol Chem, 278, 44639-44644. 102. Renault, L., Kuhlmann, J., Henkel, A. and Wittinghofer, A. (2001) Structural basis for guanine nucleotide exchange on Ran by the regulator of chromosome condensation (RCC1). Cell, 105, 245-255. 103. Edwards, T.A., Wilkinson, B.D., Wharton, R.P. and Aggarwal, A.K. (2003) Model of the brain tumor-Pumilio translation repressor complex. Genes Dev, 17, 2508-2513. 104. Bates, A.D. and Maxwell, A. (eds.) (1993) in DNA Topology. Oxford University Press, New York. 105. Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723. 106. Nollmann, M., Crisona, N.J. and Arimondo, P.B. (2007) Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism. Biochimie, 89, 490-499. 107. Ruthenburg, A.J., Graybosch, D.M., Huetsch, J.C. and Verdine, G.L. (2005) A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J Biol Chem, 280, 26177-26184. 108. Musgrave, D.R., Sandman, K.M. and Reeve, J.N. (1991) DNA binding by the archaeal histone HMf results in positive supercoiling. Proc Natl Acad Sci U S A, 88, 10397-10401. 109. Kramlinger, V.M. and Hiasa, H. (2006) The "GyrA-box" is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction. J Biol Chem, 281, 3738-3742. 110. Terwilliger, T.C. and Berendzen, J. (1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr, 55, 849-861. 111. Terwilliger, T.C. (2000) Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr, 56, 965-972. 112. Terwilliger, T.C. (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D Biol Crystallogr, 59, 38-44. 113. Terwilliger, T.C. (2003) Automated side-chain model building and sequence assignment by template matching. Acta Crystallogr D Biol Crystallogr, 59, 45-49. 114. Hellman, L.M. and Fried, M.G. (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc, 2, 1849-1861. 115. Klungsoyr, H.K. and Skarstad, K. (2004) Positive supercoiling is generated in the presence of Escherichia coli SeqA protein. Mol Microbiol, 54, 123-131. 116. Huang, Y.Y., Deng, J.Y., Gu, J., Zhang, Z.P., Maxwell, A., Bi, L.J., Chen, Y.Y., Zhou, Y.F., Yu, Z.N. and Zhang, X.E. (2006) The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA). Nucleic Acids Res, 34, 5650-5659. 117. Huang, W.M. (1996) Bacterial diversity based on type II DNA topoisomerase genes. Annu Rev Genet, 30, 79-107.
摘要: 第IIA型DNA拓撲異構酶(TopoIIAs)可催化暫時性的雙股DNA缺口產生,同時捕捉另一雙股DNA並促使其通過此缺口,從而改變DNA之拓撲構型。此酵素是維繫生命現象不可或缺的一種酵素,其活性可幫助生物體解決在DNA代謝過程中因其DNA雙股螺旋結構所衍生之DNA構型問題。大部分的細菌皆具有兩種高度同源但功能截然不同的第IIA型酵素:DNA gyrase與topoisomerase IV (TopoIV)。Gyrase可利用其主動引入DNA負超螺旋的活性來協助DNA複製及轉錄過程中起始與延長作用的進行。而TopoIV則偏好DNA 正向超螺旋的鬆弛作用(relaxation)與DNA解纏作用(DNA decatenation),主要負責將DNA複製完成後相互纏繞的子染色體解開。許多生化實驗證據強烈顯示,此兩種IIA型酵素之所以具有不同的活性與其C端domain (CTD)密切相關。然而CTD的結構如何致使二者具有不同功能則有待更多結構與生化之分析。 藉由X-光蛋白質晶體繞射分析,本論文已成功解析數個TopoIIAs CTD結構,包含噬熱性枯草桿菌TopoIV CTD (BsParC-CTD)以及大腸桿菌與十字花科黑腐病菌DNA gyrase CTD (EcGyrA-CTD 與XcGyrA-CTD);分析顯示此類型蛋白皆具有一個類似但卻不同於β-propeller的摺疊方式,稱為β-pinwheel摺疊。本論文首先報告在CTD結構上所觀察到的特徵,進而利用生化方法探討這些結構特徵對於酵素功能的影響與重要性。目前已證實一個高度保留且位於β-strand上的脯胺酸(proline) 能夠影響gyrase主動引入DNA負超螺旋的效率。此脯胺酸能扭曲GyrA-CTD的結構,導致帶有正電荷之GyrA-box motif在空間上的位移,促使其所屬的DNA結合區呈現非平面的扭曲;此特性與gyrase擁有較強的DNA纏繞及引入DNA負超螺旋能力相關。由於缺少GyrA-box motif,TopoIV CTD的DNA結合區則無此非平面的扭曲。此結構上的差異可解釋DNA gyrase 與TopoIV在生化活性上的特異性。而在β-sheet特定的位點引入脯胺酸可造成蛋白功能改變的觀念更可以應用於蛋白質工程技術。
Type IIA DNA topoisomerases (TopoIIAs) are essential and ubiquitous enzymes that catalyze ATP-dependent passage of one DNA duplex (T-segment) through a transient double-stranded breakage in another (G-segment). Such an activity alters DNA topology, allowing these enzymes to solve topological conflicts arising during cellular DNA transactions. Most bacteria harbor two closely related yet functionally distinct TopoIIAs namely DNA gyrase and TopoIV. DNA gyrase supports replication and transcription with its unique supercoiling activity, whereas TopoIV preferentially relaxes (+) supercoils and is the main decatenating enzyme required for chromosome segregation. Mounting biochemical evidences suggest that the specialized activities of DNA gyrase and Topo IV depend on their respective C-terminal domains (CTDs). However, the underlying structural mechanism remains enigmatic. Using X-ray crystallography, we have determined crystal structures of TopoIV CTD from B. stearothermophilus (BsParC-CTD) as well as the DNA gyrase CTDs from Escherichia coli (EcGyrA-CTD) and Xanthomonas campestris (XcGyrA-CTD). All of them adopt a β-propeller-like fold termed β-pinwheel. Through structural and biochemical analyses, several unique structural features of these domains have been recognized and tested for the functional relevance. In particular, we have identified a highly conserved β-strand-bearing proline located in GyrA-CTD which is crucial for gyrase to exhibit efficient (-) supercoiling activity. This proline introduces structural-twist in GyrA-CTD, which results in spatial lift of the basic GyrA-box motif and an overall non-planar DNA-binding surface suitable for unidirectional DNA wrapping. In contrast, due to the lack of GyrA-box motif, the DNA-binding surface of ParC-CTD is relatively flat. This structural difference may represent a key determinant for the functional distinction between the two bacterial TopoIIAs
URI: http://hdl.handle.net/11455/24014
其他識別: U0005-1806200914323300
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-1806200914323300
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