• Tirta Setiawan Departemen Biokimia, Fakultas Matematika dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, 16680
  • Laksmi Ambarsari 1. Departemen Biokimia, Fakultas Matematika dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, 16680 2. Pusat Penelitian Biofarmaka, Institute Pertanian Bogor, Jalan Taman Kencana No.3, Bogor 16128
  • Tony Ibnu Sumaryada Pusat Penelitian Biofarmaka, Institute Pertanian Bogor, Jalan Taman Kencana No.3, Bogor 16128 Departemen Fisika, Fakultas Matematika dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor,16680


ABSTRAK: DNA topoisomerase II (Top2) adalah enzim penting yang menangani permasalahan topologi pada DNA. Terdapat dua jenis Top2 pada manusia yaitu Top2A dan Top2B. Top2A diekspresikan pada sel yang aktif membelah seperti sel kanker sedangkan Top2B diekspresikan saat sel dalam fase istirahat. Peran penting inilah yang membuat DNA Top2A menjadi target  obat melawan kanker salah satunya obat etoposite. Sisi aktif pengikatan etoposite terhadap Top2B sudah dilakukan namun pada Top2A belum dilakukan. Studi pencarian area yang rapat dengan pensejajaran banyak sekuen pada Top2A dengan Top2B sebagai acuan bertujuan untuk pencarian sisi aktif pengikatan etoposite pada Top2A. Area yang rapat dengan kesamaan residu asam amino yang tinggi dapat digunakan untuk memprediksikan fungsi penting asam amino dalam enzim tersebut. Top2A dan Top2B memiliki kesamaan asam amino sebesar 80% dengan kesamaan struktur 71.81%. Asam amino aktif pengikatan etoposite pada Top2B Gly478, Asp479, Arg503, Met782 dan Gln778, dinyatakan mirip dan rapat terhadap residu Gly462, Asp463, Arg487, Met763 pada Top2A kecuali residu Gln778 dari Top2B namun penggantian ini tidak merubah struktur dari enzim tersebut karena sama-sama membentuk struktur alfa-heliks dan terletak pada posisi yang sama sehingga diprediksikan sisi aktif pengikatan etoposite pada enzim Top2B yaitu Gly478, Asp479, Arg503, Met782 dan Gln778memiliki fungsi yang sama dengan residu Gly462, Asp463, Arg487, Met763 dan Met767 dari Top2A. Hal ini menyebabkan etoposite juga dapat menghambat kerja enzim Top2A pada residu yang sama.


ABSTRACT: DNA topoisomerase II (Top2) is essential enzyme that solves the topological problems of DNA. Top2A and Top2B are two kind of Top2 in human. Top2A is expressed at differentiation active cells as cancer cells whereas Top2B is expressed at non differentiation cells or quiescent cells. Their critical role makes Top2B an attractive drug target against cancer as etoposite known as Top2 inhibitor. Active site for etoposite binding domain to Top2B has been done but in Top2A has not been done yet. Conserve region study by multiple sequence alignment between Top2A and Top2B as Top2B to be a template was aimed to search an active site for etoposite binding domain in Top2A. A conserve amino acid area with highest similarity was used to predict essential amino acid activity in the enzyme. Homology study shows that Top2A and Top2B have the same similarity of amino acids of 80% with  structure similarity of 71.81%. Active amino acids on Top2B for etoposite binding domain such as Gly478, Asp479, Arg503, Met782 dan Gln778 were found to be highly conserve with amino acid Gly462, Asp463, Arg487, Met763 on Top2A except Gln778 from Top2B but this does not change of structure of the enzyme because they have the same alfa-helix formations and positions so that it could be predicted that amino acids Gly478, Asp479, Arg503, Met782 and Gln778 on Top2B have similar activity and function with Gly462, Asp463, Arg487, Met763 and Met767 on Top2A.  This etoposite could inhibit the activity of the Top2A enzyme at same site.


Download data is not yet available.


[1] Nitis JL, Beck WT. 1996, “Antitopoisomerase drug action and resistance”, Eur J Cancer. 10: 68-75.
[2] Fry AM, Chresta CM, Davies SM. 1991, “Relationship between topoisomerase II level and chemosensitivity in human tumor sell lines”, Cancer Res. 51: 6592-6595.
[3] Bauman ME, Holden JA, Brown KA, Harker WG, Perkins SR. 1997, ”Differenttial immunohistochemical staining for DNA topoisomerase IIA and B in human tissue and for DNA topoisomerase IIB in non Hodkin limphoma”, Mod Pathol. 10: 168-175.
[4] Baird CL, Gordon MS, Andrenyak DM, Marecek JF, Lindsley JE. 2001,”The ATPase reaction cycle of yeast DNA topoisomerase II: slow rates of ATP resynthesis and Pi release”, J Biol Chem. 276: 27893-27898.
[5] Robinson HM, Bratlie-Thoresen S, Brown R, Gillespie DA. 2007,”Chk1 is required for G2/M check-point response induced by the catalitic topoisomerase II inhibitor ICRF-1993”, Cell Cycle. 6: 1265-1267.
[6] Chow KC, Macdonald TL, Ross WE. 1998, “DNA binding by epipodophyllo- toxins and N-acyl antracyclines: Implications for mechanism of topoisomerase inhbition”, Mol. Pharmacol. 34: 467-473.
[7] Osheroff N. 1989, “Effect of antineoplastic agent on the DNA cleavage/religation equlibrium of eukariotic topoisomerase II: inhibition of DNA religation by etoposide”, Biochemistry. 28: 6157-6160.
[8] Beck LS, Deguzman L, Lee WP, Xu Y, Siegel MW, Amento EP. 1993,”One systemic administration of transforming growth factor-beta 1 reverses age or glucocorticoid impaired wound healing”, J Clin Invest. 92: 2841-2849.
[9] Wu CC, Li TK, Far HL, Lin LY, Lin TS, YU YJ, Ten TJ, Chiang CW, Chan NL. 2011, ”Structural basis of type II topoisomerase inhibition by the anticancer drug etoposite”, J science. 333: 459-462.
[10] Kaplan E, Gunduz U. 2011, “Expression analysis of TOP2A, MSH2 adn MLH1 genes in MCF7 cells at different levels of etoposite resistance”, Eur J Pharm. 66: 29-35.
[11] Nelson D, Cox M. 2008. Principle of Biochemistry (5th Edn.). W.H. freeman and company, USA. ISBN-13: 978-0-7176-7108-1.
[12] Mount DW. 2004. Bioinformatics sequences and genome analysis. Cold Spring Harbor Laboratory Press. New York.
[13] Baxevanis AD, Ouellette BF. 2001. Bioinformatics A Practical Guide to the Analysis of Genes and Proteins Second Edition. 1-457.
[14] Golovin A, Dimitropolos D, Oldfield T, Rachedi A, Henrick K. 2005. MSDsite: a data base search and retrieval system for the analysis and viewing of bound ligands and active site. Protein. 58: 190-199.
[15] AbuHammad S, Zihlif M. 2012, “Gene expression alteration in doxorunicin resistant MCF-7 breast cancer cell line”, Genomic. 101: 213-220.
[16] Thompson JD. 1994, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice”, Nucleic Acids Res. 22: 4673–4680.
[17] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettingan PA, Mc William H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007, clustal w and clustal x version 2.0. Bioinformatic. 23: 2947-2948.
[18] Russell RB, Breed J, Barton GJ. 1992, “Conservation analysis and secondary structure prediction of the sh2 family of phosphotyrosine binding domains”, Proteins: Struct., Funct., Genet. 304, 15-20.
How to Cite
SETIAWAN, Tirta; AMBARSARI, Laksmi; SUMARYADA, Tony Ibnu. STUDI IN SILICO CONVERSE REGION ETOPOSITE BINDING DOMAIN Pada ISOZIM HUMAN DNA TOPOISOMERASE II. CAKRA KIMIA (Indonesian E-Journal of Applied Chemistry), [S.l.], v. 4, n. 1, p. 61 - 70, june 2016. ISSN 2302-7274. Available at: <>. Date accessed: 30 mar. 2023.


DNA topoisomerase; Conserve region; Multiple sequence alignment