Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Jul 25;16(14A):6447–6464. doi: 10.1093/nar/16.14.6447

Purification and enzymological characterization of DNA-dependent ATPase IV from the Novikoff hepatoma.

D C Thomas 1, D C Rein 1, R R Meyer 1
PMCID: PMC338307  PMID: 2969505

Abstract

DNA-dependent ATPase IV has been purified to near homogeneity from the Novikoff rat hepatoma. The enzyme is devoid of DNA polymerase, RNA polymerase, exonuclease, endonuclease, phosphomonoesterase, 3'- or 5'-phosphodiesterase, polynucleotide kinase, protein kinase, topoisomerase, helicase or DNA reannealing activities at a detection level of 10(-5) to 10(-7) relative to the ATPase activity. The enzyme is a monomer of Mr 110,000, has a sedimentation coefficient of 5.9 S, a Stokes radius of 40 A and a frictional coefficient of 1.32. In the presence of Mg2+ ion and a polynucleotide effector, ATPase IV hydrolyzes either ATP or dATP to the nucleoside diphosphate plus Pi. Other ribo- or deoxyribonucleoside triphosphates are not substrates. ATPase IV utilizes double-stranded DNA and single-stranded DNA as effector; however, it does not utilize poly(dT). The Km for dsDNA or ssDNA is 2.2 microM (nucleotide). A variety of ATP analogues were found to be competitive inhibitors of ATPase IV.

Full text

PDF
6447

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. ACKERS G. K. MOLECULAR EXCLUSION AND RESTRICTED DIFFUSION PROCESSES IN MOLECULAR-SIEVE CHROMATOGRAPHY. Biochemistry. 1964 May;3:723–730. doi: 10.1021/bi00893a021. [DOI] [PubMed] [Google Scholar]
  2. Assairi L. M., Johnston I. R. A DNA-dependent ATPase of calf-thymus. Eur J Biochem. 1979 Aug 15;99(1):71–79. doi: 10.1111/j.1432-1033.1979.tb13232.x. [DOI] [PubMed] [Google Scholar]
  3. Biamonti G., Cobianchi F., Falaschi A., Riva S. Total purification of a DNA-dependent ATPase and of a DNA-binding protein from human cells. EMBO J. 1983;2(2):161–165. doi: 10.1002/j.1460-2075.1983.tb01399.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bickle T. A., Pirrotta V., Imber R. A simple, general procedure for purifying restriction endonucleases. Nucleic Acids Res. 1977 Aug;4(8):2561–2572. doi: 10.1093/nar/4.8.2561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bouché J. P., Rowen L., Kornberg A. The RNA primer synthesized by primase to initiate phage G4 DNA replication. J Biol Chem. 1978 Feb 10;253(3):765–769. [PubMed] [Google Scholar]
  6. Boxer L. M., Korn D. Structural and enzymological characterization of a deoxyribonucleic acid dependent adenosine triphosphatase from KB cell nuclei. Biochemistry. 1980 Jun 10;19(12):2623–2633. doi: 10.1021/bi00553a014. [DOI] [PubMed] [Google Scholar]
  7. Cobianchi F., Riva S., Mastromei G., Spadari S., Pedrali-Noy G., Falaschi A. Enhancement of the rate of DNA polymerase-alpha activity on duplex DNA by a DNA-binding protein and a DNA-dependent ATPase of mammalian cells. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):639–647. doi: 10.1101/sqb.1979.043.01.071. [DOI] [PubMed] [Google Scholar]
  8. De Jong P. J., Tommassen J. P., Van der Vliet P. C., Jansz H. S. Purification and characterization of DNA-dependent ATP phosphohydrolases from KB cells. Eur J Biochem. 1981 Jun;117(1):179–186. doi: 10.1111/j.1432-1033.1981.tb06318.x. [DOI] [PubMed] [Google Scholar]
  9. Duguet M., Lavenot C., Harper F., Mirambeau G., De Recondo A. M. DNA topoisomerases from rat liver: physiological variations. Nucleic Acids Res. 1983 Feb 25;11(4):1059–1075. doi: 10.1093/nar/11.4.1059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Eisenberg S., Harbers B., Hours C., Denhardt D. T. The mechanism of replication of phiX174 DNA. XII. Non-random location of gaps in nascent phiX174 RF II DNA. J Mol Biol. 1975 Nov 25;99(1):107–123. doi: 10.1016/s0022-2836(75)80162-8. [DOI] [PubMed] [Google Scholar]
  11. Geider K., Hoffmann-Berling H. Proteins controlling the helical structure of DNA. Annu Rev Biochem. 1981;50:233–260. doi: 10.1146/annurev.bi.50.070181.001313. [DOI] [PubMed] [Google Scholar]
  12. Goto T., Wang J. C. Yeast DNA topoisomerase II. An ATP-dependent type II topoisomerase that catalyzes the catenation, decatenation, unknotting, and relaxation of double-stranded DNA rings. J Biol Chem. 1982 May 25;257(10):5866–5872. [PubMed] [Google Scholar]
  13. Hachmann H. J., Lezius A. G. An ATPase depending on the presence of single-stranded DNA from mouse myeloma. Eur J Biochem. 1976 Jan 15;61(2):325–330. doi: 10.1111/j.1432-1033.1976.tb10025.x. [DOI] [PubMed] [Google Scholar]
  14. Hockensmith J. W., Wahl A. F., Kowalski S., Bambara R. A. Purification of a calf thymus DNA-dependent adenosinetriphosphatase that prefers a primer-template junction effector. Biochemistry. 1986 Dec 2;25(24):7812–7821. doi: 10.1021/bi00372a005. [DOI] [PubMed] [Google Scholar]
  15. Hotta Y., Stern H. DNA unwinding protein from meiotic cells of Lilium. Biochemistry. 1978 May 16;17(10):1872–1880. doi: 10.1021/bi00603a011. [DOI] [PubMed] [Google Scholar]
  16. Hsieh T., Brutlag D. ATP-dependent DNA topoisonmerase from D. melanogaster reversibly catenates duplex DNA rings. Cell. 1980 Aug;21(1):115–125. doi: 10.1016/0092-8674(80)90119-1. [DOI] [PubMed] [Google Scholar]
  17. Hübscher U., Stalder H. P. Mammalian DNA helicase. Nucleic Acids Res. 1985 Aug 12;13(15):5471–5483. doi: 10.1093/nar/13.15.5471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kato A. C., Bartok K., Fraser M. J., Denhardt D. T. Sensitivity of superhelical DNA to a single-strand specific endonuclease. Biochim Biophys Acta. 1973 Apr 21;308(7):68–78. doi: 10.1016/0005-2787(73)90123-8. [DOI] [PubMed] [Google Scholar]
  19. Kmiec E. B., Holloman W. K. Synapsis promoted by Ustilago rec1 protein. Cell. 1984 Mar;36(3):593–598. doi: 10.1016/0092-8674(84)90338-6. [DOI] [PubMed] [Google Scholar]
  20. Kmiec E., Holloman W. K. Homologous pairing of DNA molecules promoted by a protein from Ustilago. Cell. 1982 Jun;29(2):367–374. doi: 10.1016/0092-8674(82)90153-2. [DOI] [PubMed] [Google Scholar]
  21. Koerner T. J., Meyer R. R. A novel single-stranded DNA-binding protein from the Novikoff hepatoma which stimulates DNA polymerase beta. Purification and general characterization. J Biol Chem. 1983 Mar 10;258(5):3126–3133. [PubMed] [Google Scholar]
  22. Kornberg A., Scott J. F., Bertsch L. L. ATP utilization by rep protein in the catalytic separation of DNA strands at a replicating fork. J Biol Chem. 1978 May 10;253(9):3298–3304. [PubMed] [Google Scholar]
  23. LOWRY O. H., ROSEBROUGH N. J., FARR A. L., RANDALL R. J. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951 Nov;193(1):265–275. [PubMed] [Google Scholar]
  24. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  25. MARTIN R. G., AMES B. N. A method for determining the sedimentation behavior of enzymes: application to protein mixtures. J Biol Chem. 1961 May;236:1372–1379. [PubMed] [Google Scholar]
  26. McMillan S., Edenberg H. J., Radany E. H., Friedberg R. C., Friedberg E. C. den V gene of bacteriophage T4 codes for both pyrimidine dimer-DNA glycosylase and apyrimidinic endonuclease activities. J Virol. 1981 Oct;40(1):211–223. doi: 10.1128/jvi.40.1.211-223.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Meyer R. R., Brown C. L., Rein D. C. A new DNA-dependent ATPase from Escherichia coli. Purification and characterization of ATPase IV. J Biol Chem. 1984 Apr 25;259(8):5093–5099. [PubMed] [Google Scholar]
  28. Meyer R. R., Glassberg J., Scott J. V., Kornberg A. A temperature-sensitive single-stranded DNA-binding protein from Escherichia coli. J Biol Chem. 1980 Apr 10;255(7):2897–2901. [PubMed] [Google Scholar]
  29. Meyer R. R., Simpson M. V. Deoxyribonucleic acid biosynthesis in mitochondria. Purification and general properties of rat liver mitochondrial deoxyribonucleic acid polymerase. J Biol Chem. 1970 Jul 10;245(13):3426–3435. [PubMed] [Google Scholar]
  30. Miller K. G., Liu L. F., Englund P. T. A homogeneous type II DNA topoisomerase from HeLa cell nuclei. J Biol Chem. 1981 Sep 10;256(17):9334–9339. [PubMed] [Google Scholar]
  31. Mosbaugh D. W., Meyer R. R. Interaction of mammalian deoxyribonuclease V, a double strand 3' to 5' and 5' to 3' exonuclease, with deoxyribonucleic acid polymerase-beta from the Novikoff hepatoma. J Biol Chem. 1980 Nov 10;255(21):10239–10247. [PubMed] [Google Scholar]
  32. Ottiger H. P., Hübscher U. Mammalian DNA polymerase alpha holoenzymes with possible functions at the leading and lagging strand of the replication fork. Proc Natl Acad Sci U S A. 1984 Jul;81(13):3993–3997. doi: 10.1073/pnas.81.13.3993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Otto B. DNA-dependent ATPases in concanavalin A stimulated lymphocytes. FEBS Lett. 1977 Jul 1;79(1):175–178. doi: 10.1016/0014-5793(77)80377-3. [DOI] [PubMed] [Google Scholar]
  34. Plevani P., Badaracco G., Chang L. M. Purification and characterization of two forms of DNA-dependent ATPase from yeast. J Biol Chem. 1980 May 25;255(10):4957–4963. [PubMed] [Google Scholar]
  35. Rhodes G., Jentsch K. D., Jovin T. M. A simple and rapid purification method for Escherichia coli DNA polymerase I. J Biol Chem. 1979 Aug 25;254(16):7465–7467. [PubMed] [Google Scholar]
  36. Richet E., Kohiyama M. Purification and characterization of DNA-dependent ATPase II from Escherichia coli. J Biol Chem. 1978 Oct 25;253(20):7490–7495. [PubMed] [Google Scholar]
  37. Rowen L., Kornberg A. Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains. J Biol Chem. 1978 Feb 10;253(3):758–764. [PubMed] [Google Scholar]
  38. Rubin C. S., Erlichman J., Rosen O. M. Cyclic AMP-dependent protein kinase from bovine heart muscle. Methods Enzymol. 1974;38:308–315. doi: 10.1016/0076-6879(74)38047-0. [DOI] [PubMed] [Google Scholar]
  39. SCHACHMAN H. K., ADLER J., RADDING C. M., LEHMAN I. R., KORNBERG A. Enzymatic synthesis of deoxyribonucleic acid. VII. Synthesis of a polymer of deoxyadenylate and deoxythymidylate. J Biol Chem. 1960 Nov;235:3242–3249. [PubMed] [Google Scholar]
  40. Sander M., Hsieh T. Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. J Biol Chem. 1983 Jul 10;258(13):8421–8428. [PubMed] [Google Scholar]
  41. Seki M., Enomoto T., Yanagisawa J., Hanaoka F., Ui M. Further characterization of DNA helicase activity of mouse DNA-dependent adenosinetriphosphatase B (DNA helicase B). Biochemistry. 1988 Mar 8;27(5):1766–1771. doi: 10.1021/bi00405a057. [DOI] [PubMed] [Google Scholar]
  42. Siegel L. M., Monty K. J. Determination of molecular weights and frictional ratios of proteins in impure systems by use of gel filtration and density gradient centrifugation. Application to crude preparations of sulfite and hydroxylamine reductases. Biochim Biophys Acta. 1966 Feb 7;112(2):346–362. doi: 10.1016/0926-6585(66)90333-5. [DOI] [PubMed] [Google Scholar]
  43. Stalker D. M., Mosbaugh D. W., Meyer R. R. Novikoff hepatoma deoxyribonucleic acid polymerase. Purification and properties of a homogeneous beta polymerase. Biochemistry. 1976 Jul 13;15(14):3114–3121. doi: 10.1021/bi00659a027. [DOI] [PubMed] [Google Scholar]
  44. TOMLINSON R. V., TENER G. M. THE EFFECT OF UREA, FORMAMIDE, AND GLYCOLS ON THE SECONDARY BINDING FORCES IN THE ION-EXCHANGE CHROMATOGRAPHY OF POLYNUCLEOTIDES OF DEAE-CELLULOSE. Biochemistry. 1963 Jul-Aug;2:697–702. doi: 10.1021/bi00904a013. [DOI] [PubMed] [Google Scholar]
  45. Tawaragi Y., Enomoto T., Watanabe Y., Hanaoka F., Yamada M. Multiple deoxyribonucleic acid dependent adenosinetriphosphatases in FM3A cells. Characterization of an adenosinetriphosphatase that prefers poly [d(A-T)] as cofactor. Biochemistry. 1984 Jan 31;23(3):529–533. doi: 10.1021/bi00298a020. [DOI] [PubMed] [Google Scholar]
  46. Thomas D. C., Meyer R. R. Deoxyribonucleic acid dependent adenosinetriphosphatases from the Novikoff hepatoma. Characterization of a homogeneous adenosinetriphosphatase that stimulates DNA polymerase beta. Biochemistry. 1982 Sep 28;21(20):5060–5068. doi: 10.1021/bi00263a033. [DOI] [PubMed] [Google Scholar]
  47. Yaginuma K., Koike K. Properties of a DNA-dependent ATPase from rat mitochondria. Nucleic Acids Res. 1981 Apr 24;9(8):1949–1961. doi: 10.1093/nar/9.8.1949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Yarranton G. T., Das R. H., Gefter M. L. Enzyme-catalyzed DNA unwinding. Mechanism of action of helicase III. J Biol Chem. 1979 Dec 10;254(23):12002–12006. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES