Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Nov 11;16(21):9909–9916. doi: 10.1093/nar/16.21.9909

A sequence motif in many polymerases.

P Argos 1
PMCID: PMC338826  PMID: 2461550

Abstract

A 15-residue sequence motif has been found in many polymerases from various species and involving DNA and RNA dependence and product. The motif is characterized by a Tyr-Gly-Asp-(Thr)-Asp core flanked by hydrophobic spans five residues in length. An mRNA maturase segment is also suggested to display the motif pattern. The aspartates may be important in polymerase function by acting directly in catalysis and/or by binding magnesium.

Full text

PDF
9911

Selected References

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

  1. Allison L. A., Moyle M., Shales M., Ingles C. J. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell. 1985 Sep;42(2):599–610. doi: 10.1016/0092-8674(85)90117-5. [DOI] [PubMed] [Google Scholar]
  2. Argos P. Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis. J Mol Biol. 1987 Sep 20;197(2):331–348. doi: 10.1016/0022-2836(87)90127-6. [DOI] [PubMed] [Google Scholar]
  3. Argos P. Evidence for a repeating domain in type I restriction enzymes. EMBO J. 1985 May;4(5):1351–1355. doi: 10.1002/j.1460-2075.1985.tb03784.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Armaleo D. Structure and evolution of prokaryotic and eukaryotic RNA polymerases: a model. J Theor Biol. 1987 Aug 7;127(3):301–314. doi: 10.1016/s0022-5193(87)80108-x. [DOI] [PubMed] [Google Scholar]
  5. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  6. Boccardo G., Accotto G. P. RNA-dependent RNA polymerase activity in two morphologically different white clover cryptic viruses. Virology. 1988 Apr;163(2):413–419. doi: 10.1016/0042-6822(88)90282-6. [DOI] [PubMed] [Google Scholar]
  7. Davison A. J., Scott J. E. The complete DNA sequence of varicella-zoster virus. J Gen Virol. 1986 Sep;67(Pt 9):1759–1816. doi: 10.1099/0022-1317-67-9-1759. [DOI] [PubMed] [Google Scholar]
  8. Falkenburg D., Dworniczak B., Faust D. M., Bautz E. K. RNA polymerase II of Drosophila. Relation of its 140,000 Mr subunit to the beta subunit of Escherichia coli RNA polymerase. J Mol Biol. 1987 Jun 20;195(4):929–937. doi: 10.1016/0022-2836(87)90496-7. [DOI] [PubMed] [Google Scholar]
  9. Forster R. L., Bevan M. W., Harbison S. A., Gardner R. C. The complete nucleotide sequence of the potexvirus white clover mosaic virus. Nucleic Acids Res. 1988 Jan 11;16(1):291–303. doi: 10.1093/nar/16.1.291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hardman K. D., Ainsworth C. F. Structure of concanavalin A at 2.4-A resolution. Biochemistry. 1972 Dec 19;11(26):4910–4919. doi: 10.1021/bi00776a006. [DOI] [PubMed] [Google Scholar]
  11. Hizi A., McGill C., Hughes S. H. Expression of soluble, enzymatically active, human immunodeficiency virus reverse transcriptase in Escherichia coli and analysis of mutants. Proc Natl Acad Sci U S A. 1988 Feb;85(4):1218–1222. doi: 10.1073/pnas.85.4.1218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hodgman T. C. An amino acid sequence motif linking viral DNA polymerases and plant virus proteins involved in RNA replication. Nucleic Acids Res. 1986 Aug 26;14(16):6769–6769. doi: 10.1093/nar/14.16.6769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Inokuchi Y., Hirashima A. Interference with viral infection by defective RNA replicase. J Virol. 1987 Dec;61(12):3946–3949. doi: 10.1128/jvi.61.12.3946-3949.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Johnson M. S., McClure M. A., Feng D. F., Gray J., Doolittle R. F. Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7648–7652. doi: 10.1073/pnas.83.20.7648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Jung G. H., Leavitt M. C., Hsieh J. C., Ito J. Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8287–8291. doi: 10.1073/pnas.84.23.8287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Jurnak F. Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins. Science. 1985 Oct 4;230(4721):32–36. doi: 10.1126/science.3898365. [DOI] [PubMed] [Google Scholar]
  17. Kamer G., Argos P. Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res. 1984 Sep 25;12(18):7269–7282. doi: 10.1093/nar/12.18.7269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Katinka M. D. RNA-dependent DNA polymerase activity in Paramecium tetraurelia: what for? Eur J Biochem. 1987 Mar 16;163(3):569–575. doi: 10.1111/j.1432-1033.1987.tb10905.x. [DOI] [PubMed] [Google Scholar]
  19. Lazowska J., Jacq C., Slonimski P. P. Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron. Cell. 1980 Nov;22(2 Pt 2):333–348. doi: 10.1016/0092-8674(80)90344-x. [DOI] [PubMed] [Google Scholar]
  20. Ollis D. L., Brick P., Hamlin R., Xuong N. G., Steitz T. A. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. 1985 Feb 28-Mar 6Nature. 313(6005):762–766. doi: 10.1038/313762a0. [DOI] [PubMed] [Google Scholar]
  21. Ovchinnikov Y. A., Monastyrskaya G. S., Gubanov V. V., Guryev S. O., Chertov OYu, Modyanov N. N., Grinkevich V. A., Makarova I. A., Marchenko T. V., Polovnikova I. N. The primary structure of Escherichia coli RNA polymerase. Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit. Eur J Biochem. 1981 Jun 1;116(3):621–629. doi: 10.1111/j.1432-1033.1981.tb05381.x. [DOI] [PubMed] [Google Scholar]
  22. Panka D., Dennis D. RNA polymerase. Direct evidence for two active sites involved in transcription. J Biol Chem. 1985 Feb 10;260(3):1427–1431. [PubMed] [Google Scholar]
  23. Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986 Sep;5(9):2043–2049. doi: 10.1002/j.1460-2075.1986.tb04464.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Sidman K. E., George D. G., Barker W. C., Hunt L. T. The protein identification resource (PIR). Nucleic Acids Res. 1988 Mar 11;16(5):1869–1871. doi: 10.1093/nar/16.5.1869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sweetser D., Nonet M., Young R. A. Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc Natl Acad Sci U S A. 1987 Mar;84(5):1192–1196. doi: 10.1073/pnas.84.5.1192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tanese N., Sodroski J., Haseltine W. A., Goff S. P. Expression of reverse transcriptase activity of human T-lymphotropic virus type III (HTLV-III/LAV) in Escherichia coli. J Virol. 1986 Sep;59(3):743–745. doi: 10.1128/jvi.59.3.743-745.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Watson H. C., Walker N. P., Shaw P. J., Bryant T. N., Wendell P. L., Fothergill L. A., Perkins R. E., Conroy S. C., Dobson M. J., Tuite M. F. Sequence and structure of yeast phosphoglycerate kinase. EMBO J. 1982;1(12):1635–1640. doi: 10.1002/j.1460-2075.1982.tb01366.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wong S. W., Wahl A. F., Yuan P. M., Arai N., Pearson B. E., Arai K., Korn D., Hunkapiller M. W., Wang T. S. Human DNA polymerase alpha gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. EMBO J. 1988 Jan;7(1):37–47. doi: 10.1002/j.1460-2075.1988.tb02781.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Wu S. X., Rinehart C. A., Kaesberg P. Sequence and organization of southern bean mosaic virus genomic RNA. Virology. 1987 Nov;161(1):73–80. doi: 10.1016/0042-6822(87)90172-3. [DOI] [PubMed] [Google Scholar]

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

RESOURCES