Home LiteratureArticle Details
PMID: 9094674 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Purification of the simian virus 40 (SV40) T antigen DNA-binding domain and characterization of its interactions with the SV40 origin.

Journal of virology ·Vol. 71 ·No. 5 ·1997-05-00 ·Pages 3972-85

Joo WS, Luo X, Denis D, Kim HY, Rainey GJ, Jones C, Sreekumar KR, Bullock PA

Abstract

To better define protein-DNA interactions at a eukaryotic origin, the domain of simian virus 40 (SV40) large T antigen that specifically interacts with the SV40 origin has been purified and its binding to DNA has been characterized. Evidence is presented that the affinity of the purified T antigen DNA-binding domain for the SV40 origin is comparable to that of the full-length T antigen. Furthermore, stable binding of the T antigen DNA-binding domain to the SV40 origin requires pairs of pentanucleotide recognition sites separated by approximately one turn of a DNA double helix and positioned in a head-to-head orientation. Although two pairs of pentanucleotides are present in the SV40 origin, footprinting and band shift experiments indicate that binding is limited to dimer formation on a single pair of pentanucleotides. Finally, it is demonstrated that the T antigen DNA-binding domain interacts poorly with single-stranded DNA.

MeSH Terms
Antigens, Polyomavirus Transforming/chemistry,metabolism Base Sequence Binding Sites DNA/metabolism Molecular Sequence Data Peptide Fragments/isolation & purification,metabolism Simian virus 40/immunology
Chemicals
Antigens, Polyomavirus Transforming Peptide Fragments DNA
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Joo W S
Department of Biochemistry, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
Luo X
Denis D
Kim H Y
Rainey G J
Jones C
Sreekumar K R
Bullock P A
References (86)
86 references, click to expand
  1. ATP-dependent assembly of double hexamers of SV40 T antigen at the viral origin of DNA replication.
    Nature. 1989 Apr 20;338(6217):658-62 PMID: 2539565
  2. Initiation of simian virus 40 DNA replication in vitro: pulse-chase experiments identify the first labeled species as topologically unwound.
    Proc Natl Acad Sci U S A. 1989 Jun;86(11):3944-8 PMID: 2542958
  3. Animal virus DNA replication.
    Annu Rev Biochem. 1989;58:671-717 PMID: 2549858
  4. Large T-antigen mutants define multiple steps in the initiation of simian virus 40 DNA replication.
    J Virol. 1989 Oct;63(10):4181-8 PMID: 2550664
  5. Properties of the DNA-binding domain of the simian virus 40 large T antigen.
    Mol Cell Biol. 1989 Dec;9(12):5525-36 PMID: 2555700
  6. Initiation of eukaryotic DNA replication in vitro.
    Annu Rev Cell Biol. 1989;5:197-245 PMID: 2557059
  7. Three domains in the simian virus 40 core origin orchestrate the binding, melting, and DNA helicase activities of T antigen.
    J Virol. 1990 Feb;64(2):509-18 PMID: 2153220
  8. Binding and unwinding--how T antigen engages the SV40 origin of DNA replication.
    Cell. 1990 Jan 26;60(2):181-4 PMID: 2153460
  9. Four major sequence elements of simian virus 40 large T antigen coordinate its specific and nonspecific DNA binding.
    J Virol. 1990 May;64(5):1973-83 PMID: 2157865
  10. Mapping of helicase and helicase substrate-binding domains on simian virus 40 large T antigen.
    J Virol. 1990 May;64(5):2014-20 PMID: 2157869
  11. Identification of simian virus 40 T-antigen residues important for specific and nonspecific binding to DNA and for helicase activity.
    J Virol. 1990 Oct;64(10):4858-65 PMID: 2168972
  12. Simian virus 40 T antigen is required for viral excision from chromosomes.
    Proc Natl Acad Sci U S A. 1984 Dec;81(23):7534-8 PMID: 6095304
  13. Purification of simian virus 40 large T antigen by immunoaffinity chromatography.
    J Virol. 1985 Mar;53(3):1001-4 PMID: 2983081
  14. Sequence-specific binding of simian virus 40 A protein to nonorigin and cellular DNA.
    Mol Cell Biol. 1984 Dec;4(12):2631-8 PMID: 6570189
  15. The DNA enzymology of protein machines.
    Cold Spring Harb Symp Quant Biol. 1984;49:1-12 PMID: 6597749
  16. Monomers through trimers of large tumor antigen bind in region I and monomers through tetramers bind in region II of simian virus 40 origin of replication DNA as stable structures in solution.
    Proc Natl Acad Sci U S A. 1985 Jun;82(11):3626-30 PMID: 2987937
  17. Seventeen base pairs of region I encode a novel tripartite binding signal for SV40 T antigen.
    Cell. 1985 Sep;42(2):539-48 PMID: 2992803
  18. In vitro replication of duplex circular DNA containing the simian virus 40 DNA origin site.
    Proc Natl Acad Sci U S A. 1985 Sep;82(17):5710-4 PMID: 2994044
  19. An immunoaffinity purification procedure for SV40 large T antigen.
    Virology. 1985 Jul 15;144(1):88-100 PMID: 2998049
  20. T antigen and template requirements for SV40 DNA replication in vitro.
    EMBO J. 1985 Nov;4(11):2933-9 PMID: 2998767
  21. Simian virus 40 origin DNA-binding domain on large T antigen.
    J Virol. 1986 Jan;57(1):50-64 PMID: 3001365
  22. Guanine nucleotide contacts within viral DNA sequences bound by polyomavirus large T antigen.
    J Virol. 1986 Feb;57(2):505-14 PMID: 3003383
  23. The in vitro replication of DNA containing the SV40 origin.
    J Biol Chem. 1990 Oct 25;265(30):18043-6 PMID: 1976634
  24. The finger domain of simian virus 40 large T antigen controls DNA-binding specificity.
    J Virol. 1990 Dec;64(12):6291-6 PMID: 2173794
  25. Simian virus 40 large T antigen untwists DNA at the origin of DNA replication.
    J Biol Chem. 1991 Mar 15;266(8):5062-71 PMID: 1848235
  26. Cooperative assembly of simian virus 40 T-antigen hexamers on functional halves of the replication origin.
    J Virol. 1991 Jun;65(6):2798-806 PMID: 1851855
  27. Simian virus 40 large T antigen: the puzzle, the pieces, and the emerging picture.
    J Virol. 1992 Mar;66(3):1289-93 PMID: 1310750
  28. Spacing is crucial for coordination of domain functions within the simian virus 40 core origin of replication.
    J Virol. 1992 Apr;66(4):1933-42 PMID: 1312612
  29. The simian virus 40 T antigen double hexamer assembles around the DNA at the replication origin.
    J Biol Chem. 1992 Jul 15;267(20):14129-37 PMID: 1321135
  30. Structure and function of simian virus 40 large tumor antigen.
    Annu Rev Biochem. 1992;61:55-85 PMID: 1323237
  31. Nonspecific DNA binding activity of simian virus 40 large T antigen: evidence for the cooperation of two regions for full activity.
    J Virol. 1992 Sep;66(9):5443-52 PMID: 1323705
  32. Mechanism of activation of simian virus 40 DNA replication by protein phosphatase 2A.
    Mol Cell Biol. 1992 Nov;12(11):4883-95 PMID: 1328866
  33. Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target.
    Nature. 1992 Oct 8;359(6395):505-12 PMID: 1328886
  34. Transcriptional activation by simian virus 40 large T antigen: interactions with multiple components of the transcription complex.
    Mol Cell Biol. 1993 Feb;13(2):961-9 PMID: 8423815
  35. DNA polymerase alpha stimulates the ATP-dependent binding of simian virus tumor T antigen to the SV40 origin of replication.
    J Biol Chem. 1993 May 25;268(15):11018-27 PMID: 8388381
  36. Biochemical analysis of mutants with changes in the origin-binding domain of simian virus 40 tumor antigen.
    J Virol. 1993 Jul;67(7):4227-36 PMID: 8389924
  37. Cooperative assembly of the bovine papilloma virus E1 and E2 proteins on the replication origin requires an intact E2 binding site.
    J Biol Chem. 1993 Jul 25;268(21):15795-803 PMID: 8393453
  38. Eukaryotic DNA replication: anatomy of an origin.
    Annu Rev Biochem. 1993;62:29-63 PMID: 8352592
  39. The DNA-binding domain of simian virus 40 tumor antigen has multiple functions.
    J Virol. 1993 Dec;67(12):7608-11 PMID: 8230479
  40. Mapping initiation sites for simian virus 40 DNA synthesis events in vitro.
    Mol Cell Biol. 1994 Aug;14(8):5043-55 PMID: 8035788
  41. The origin recognition complex interacts with a bipartite DNA binding site within yeast replicators.
    Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2224-8 PMID: 7892251
  42. Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein, EBNA1, bound to DNA.
    Cell. 1996 Mar 8;84(5):791-800 PMID: 8625416
  43. Mechanisms of simian virus 40 T-antigen activation by phosphorylation of threonine 124.
    J Virol. 1996 Jun;70(6):3887-93 PMID: 8648725
  44. Solution structure of the origin DNA-binding domain of SV40 T-antigen.
    Nat Struct Biol. 1996 Dec;3(12):1034-9 PMID: 8946857
  45. Simian virus 40 deoxyribonucleic acid synthesis: the viral replicon.
    J Virol. 1972 Oct;10(4):591-8 PMID: 4343541
  46. The binding site on SV40 DNA for a T antigen-related protein.
    Cell. 1978 Jan;13(1):165-79 PMID: 202398
  47. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  48. Single strand DNA binding of simian virus 40 tumor antigen.
    J Biol Chem. 1979 Apr 25;254(8):3100-4 PMID: 218962
  49. Regulatory mutants of simian virus 40: constructed mutants with base substitutions at the origin of DNA replication.
    J Mol Biol. 1979 Jul 15;131(4):801-17 PMID: 229233
  50. Sequencing end-labeled DNA with base-specific chemical cleavages.
    Methods Enzymol. 1980;65(1):499-560 PMID: 6246368
  51. Amino acid sequence analysis of fragments generated by partial proteolysis from large simian virus 40 tumor antigen.
    J Biol Chem. 1980 Jun 25;255(12):5627-34 PMID: 6247340
  52. Mapping of SV40 DNA replication origin region binding sites for the SV40 T antigen by protection against exonuclease III digestion.
    Cell. 1980 Jun;20(2):411-22 PMID: 6248243
  53. Construction and analysis of simian virus 40 origins defective in tumor antigen binding and DNA replication.
    Proc Natl Acad Sci U S A. 1980 Nov;77(11):6491-5 PMID: 6256739
  54. Topography of simian virus 40 A protein-DNA complexes: arrangement of pentanucleotide interaction sites at the origin of replication.
    J Virol. 1983 Apr;46(1):143-50 PMID: 6298451
  55. Topography of simian virus 40 A protein-DNA complexes: arrangement of protein bound to the origin of replication.
    J Virol. 1983 Apr;46(1):151-61 PMID: 6298452
  56. Nucleotide sequence of the region encompassing the JC virus origin of DNA replication.
    J Virol. 1983 Apr;46(1):170-6 PMID: 6298454
  57. Binding of SV40 a protein to the BK virus origin of DNA replication.
    Virology. 1983 Aug;129(1):239-45 PMID: 6310883
  58. Binding of simian virus 40 a protein to DNA with deletions at the origin of replication.
    J Virol. 1984 Jan;49(1):9-13 PMID: 6317897
  59. Essential contact residues within SV40 large T antigen binding sites I and II identified by alkylation-interference.
    Cell. 1984 Jan;36(1):155-62 PMID: 6319005
  60. Critical spatial requirement within the origin of simian virus 40 DNA replication.
    J Virol. 1984 Jul;51(1):91-6 PMID: 6328047
  61. An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen.
    Cell. 1986 Mar 14;44(5):719-25 PMID: 3004744
  62. DNA-binding region of the simian virus 40 tumor antigen.
    J Virol. 1986 Mar;57(3):776-85 PMID: 3005626
  63. Affinity purification of sequence-specific DNA binding proteins.
    Proc Natl Acad Sci U S A. 1986 Aug;83(16):5889-93 PMID: 3461465
  64. Multiple DNA-protein interactions governing high-precision DNA transactions.
    Science. 1986 Sep 5;233(4768):1050-6 PMID: 2943018
  65. DNA helicase activity of SV40 large tumor antigen.
    EMBO J. 1986 Aug;5(8):1939-44 PMID: 3019672
  66. Functional organization of the simian virus 40 origin of DNA replication.
    Mol Cell Biol. 1986 Apr;6(4):1117-28 PMID: 3023870
  67. Domain structure of the simian virus 40 core origin of replication.
    Mol Cell Biol. 1986 May;6(5):1663-70 PMID: 3023900
  68. Simian virus 40 (SV40) DNA replication: SV40 large T antigen unwinds DNA containing the SV40 origin of replication.
    Proc Natl Acad Sci U S A. 1987 Jan;84(1):16-20 PMID: 3025851
  69. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction.
    Cold Spring Harb Symp Quant Biol. 1986;51 Pt 1:263-73 PMID: 3472723
  70. The T-antigen-binding domain of the simian virus 40 core origin of replication.
    J Virol. 1987 Jul;61(7):2143-9 PMID: 3035215
  71. Initiation of simian virus 40 DNA replication in vitro: large-tumor-antigen- and origin-dependent unwinding of the template.
    Proc Natl Acad Sci U S A. 1987 Jun;84(11):3643-7 PMID: 3035543
  72. Consensus topography in the ATP binding site of the simian virus 40 and polyomavirus large tumor antigens.
    Proc Natl Acad Sci U S A. 1987 Jun;84(12):4026-30 PMID: 3035562
  73. Studies on the origin-specific DNA-binding domain of simian virus 40 large T antigen.
    J Virol. 1987 Oct;61(10):3326-30 PMID: 3041053
  74. Unwinding of duplex DNA from the SV40 origin of replication by T antigen.
    Science. 1987 Nov 13;238(4829):964-7 PMID: 2823389
  75. ATP enhances the binding of simian virus 40 large T antigen to the origin of replication.
    J Virol. 1987 Dec;61(12):3649-54 PMID: 2824805
  76. The unwinding of duplex regions in DNA by the simian virus 40 large tumor antigen-associated DNA helicase activity.
    J Biol Chem. 1988 Jan 5;263(1):383-92 PMID: 2826443
  77. ATP-dependent formation of a specialized nucleoprotein structure by simian virus 40 (SV40) large tumor antigen at the SV40 replication origin.
    Proc Natl Acad Sci U S A. 1987 Dec;84(24):8981-5 PMID: 2827164
  78. Footprinting DNA-protein complexes in situ following gel retardation assays using 1,10-phenanthroline-copper ion: Escherichia coli RNA polymerase-lac promoter complexes.
    Biochemistry. 1987 Nov 17;26(23):7234-8 PMID: 3322397
  79. ATP stimulates the binding of simian virus 40 (SV40) large tumor antigen to the SV40 origin of replication.
    Proc Natl Acad Sci U S A. 1988 Jan;85(1):64-8 PMID: 2829177
  80. Geometry of the simian virus 40 large tumor antigen-DNA complex as probed by protease digestion.
    Proc Natl Acad Sci U S A. 1988 Apr;85(7):2086-90 PMID: 2832846
  81. Expression of simian virus 40 T antigen in Escherichia coli: localization of T-antigen origin DNA-binding domain to within 129 amino acids.
    J Virol. 1988 Jun;62(6):1999-2006 PMID: 2835505
  82. Simian virus 40 (SV40) T antigen binds specifically to double-stranded DNA but not to single-stranded DNA or DNA/RNA hybrids containing the SV40 regulatory sequences.
    J Virol. 1988 Jun;62(6):2204-8 PMID: 3367427
  83. Sequence specificity of DNA cleavage by bis(1,10-phenanthroline)copper(I).
    Biochemistry. 1988 Mar 22;27(6):1822-7 PMID: 3378032
  84. Expression and complex formation of simian virus 40 large T antigen and mouse p53 in insect cells.
    J Virol. 1988 Sep;62(9):3109-19 PMID: 2457111
  85. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase.
    Gene. 1988 Jul 15;67(1):31-40 PMID: 3047011
  86. Localized melting and structural changes in the SV40 origin of replication induced by T-antigen.
    EMBO J. 1988 Oct;7(10):3149-58 PMID: 2846276
Article Info
Journal
Journal of virology
Abbr.
J Virol
ISSN
0022-538X
DOI
10.1128/JVI.71.5.3972-3985.1997
Published
1997-05-00
Pages
3972-85
Language
English
Region
United States
NLM ID
0113724
PMCID
PMC191549
Subset
IM
Grants
NIAID NIH HHS · R01 AI30032 · United States
External Links
PubMed source DOI: 10.1128/JVI.71.5.3972-3985.1997 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2