Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1994 Nov 8;91(23):10972–10976. doi: 10.1073/pnas.91.23.10972

The DNA-binding domain of the MotA transcription factor from bacteriophage T4 shows structural similarity to the TATA-binding protein.

M S Finnin 1, D W Hoffman 1, S W White 1
PMCID: PMC45148  PMID: 7971994

Abstract

The bacteriophage T4 middle-mode transcription factor MotA consists of two domains of approximately equal size. The C-terminal domain has been shown to contain the DNA-binding elements of the molecule, and the N-terminal domain appears to interact with RNA polymerase. A 12.5-kDa fragment of the C-terminal domain (MotCF), comprising residues 105-211 of MotA, was found to be suitable for structural studies by NMR. The 1H and 15N assignments have been made for MotCF by using two-dimensional homonuclear and heteronuclear experiments. A secondary structure has been determined which consists of a six-stranded antiparallel beta-pleated sheet with three alpha-helical segments. The secondary structure of MotCF has a clear similarity to one half of the eukaryotic TATA-binding protein (TBP), which is an intramolecular dimer. Therefore, MotCF may be related to a monomeric ancestral protein of TBP. TBP binds its target DNA in the minor groove by specific interactions with hydrophobic and aromatic residues on the exposed sheet surface of the protein. Similar residues are also present on the beta-sheet surface of MotCF, suggesting that it too binds DNA in the minor groove.

Full text

PDF
10972

Images in this article

10976Image
on p.10976

Selected References

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

  1. Aggarwal A. K., Rodgers D. W., Drottar M., Ptashne M., Harrison S. C. Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science. 1988 Nov 11;242(4880):899–907. doi: 10.1126/science.3187531. [DOI] [PubMed] [Google Scholar]
  2. Benson K. H., Kreuzer K. N. Role of MotA transcription factor in bacteriophage T4 DNA replication. J Mol Biol. 1992 Nov 5;228(1):88–100. doi: 10.1016/0022-2836(92)90493-4. [DOI] [PubMed] [Google Scholar]
  3. Bernstein H., Bernstein C. Bacteriophage T4 genetic homologies with bacteria and eucaryotes. J Bacteriol. 1989 May;171(5):2265–2270. doi: 10.1128/jb.171.5.2265-2270.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chasman D. I., Flaherty K. M., Sharp P. A., Kornberg R. D. Crystal structure of yeast TATA-binding protein and model for interaction with DNA. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):8174–8178. doi: 10.1073/pnas.90.17.8174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Ferré-D'Amaré A. R., Burley S. K. Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies. Structure. 1994 May 15;2(5):357–359. doi: 10.1016/s0969-2126(00)00037-x. [DOI] [PubMed] [Google Scholar]
  6. Finnin M. S., Hoffman D. W., Kreuzer K. N., Porter S. J., Schmidt R. P., White S. W. The MotA protein from bacteriophage T4 contains two domains. Preliminary structural analysis by X-ray diffraction and nuclear magnetic resonance. J Mol Biol. 1993 Jul 5;232(1):301–304. doi: 10.1006/jmbi.1993.1384. [DOI] [PubMed] [Google Scholar]
  7. Gronenborn A. M., Bax A., Wingfield P. T., Clore G. M. A powerful method of sequential proton resonance assignment in proteins using relayed 15N-1H multiple quantum coherence spectroscopy. FEBS Lett. 1989 Jan 16;243(1):93–98. doi: 10.1016/0014-5793(89)81224-4. [DOI] [PubMed] [Google Scholar]
  8. Guild N., Gayle M., Sweeney R., Hollingsworth T., Modeer T., Gold L. Transcriptional activation of bacteriophage T4 middle promoters by the motA protein. J Mol Biol. 1988 Jan 20;199(2):241–258. doi: 10.1016/0022-2836(88)90311-7. [DOI] [PubMed] [Google Scholar]
  9. Hinton D. M. Transcription from a bacteriophage T4 middle promoter using T4 motA protein and phage-modified RNA polymerase. J Biol Chem. 1991 Sep 25;266(27):18034–18044. [PubMed] [Google Scholar]
  10. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. doi: 10.1038/365520a0. [DOI] [PubMed] [Google Scholar]
  11. Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. doi: 10.1038/365512a0. [DOI] [PubMed] [Google Scholar]
  12. Liebig H. D., Rüger W. Bacteriophage T4 early promoter regions. Consensus sequences of promoters and ribosome-binding sites. J Mol Biol. 1989 Aug 20;208(4):517–536. doi: 10.1016/0022-2836(89)90145-9. [DOI] [PubMed] [Google Scholar]
  13. Luisi B. F., Xu W. X., Otwinowski Z., Freedman L. P., Yamamoto K. R., Sigler P. B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 1991 Aug 8;352(6335):497–505. doi: 10.1038/352497a0. [DOI] [PubMed] [Google Scholar]
  14. Marion D., Wüthrich K. Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H-1H spin-spin coupling constants in proteins. Biochem Biophys Res Commun. 1983 Jun 29;113(3):967–974. doi: 10.1016/0006-291x(83)91093-8. [DOI] [PubMed] [Google Scholar]
  15. Mattson T., Richardson J., Goodin D. Mutant of bacteriophage T4D affecting expression of many early genes. Nature. 1974 Jul 5;250(461):48–50. doi: 10.1038/250048a0. [DOI] [PubMed] [Google Scholar]
  16. Mattson T., Van Houwe G., Epstein R. H. Isolation and characterization of conditional lethal mutations in the mot gene of bacteriophage T4. J Mol Biol. 1978 Dec 15;126(3):551–570. doi: 10.1016/0022-2836(78)90058-x. [DOI] [PubMed] [Google Scholar]
  17. Menkens A. E., Kreuzer K. N. Deletion analysis of bacteriophage T4 tertiary origins. A promoter sequence is required for a rifampicin-resistant replication origin. J Biol Chem. 1988 Aug 15;263(23):11358–11365. [PubMed] [Google Scholar]
  18. Mondragón A., Harrison S. C. The phage 434 Cro/OR1 complex at 2.5 A resolution. J Mol Biol. 1991 May 20;219(2):321–334. doi: 10.1016/0022-2836(91)90568-q. [DOI] [PubMed] [Google Scholar]
  19. Nikolov D. B., Hu S. H., Lin J., Gasch A., Hoffmann A., Horikoshi M., Chua N. H., Roeder R. G., Burley S. K. Crystal structure of TFIID TATA-box binding protein. Nature. 1992 Nov 5;360(6399):40–46. doi: 10.1038/360040a0. [DOI] [PubMed] [Google Scholar]
  20. O'Farrell P. Z., Gold L. M. Transcription and translation of prereplicative bacteriophage T4 genes in vitro. J Biol Chem. 1973 Aug 10;248(15):5512–5519. [PubMed] [Google Scholar]
  21. Schmidt R. P., Kreuzer K. N. Purified MotA protein binds the -30 region of a bacteriophage T4 middle-mode promoter and activates transcription in vitro. J Biol Chem. 1992 Jun 5;267(16):11399–11407. [PubMed] [Google Scholar]
  22. Uzan M., Brody E., Favre R. Nucleotide sequence and control of transcription of the bacteriophage T4 motA regulatory gene. Mol Microbiol. 1990 Sep;4(9):1487–1496. doi: 10.1111/j.1365-2958.1990.tb02059.x. [DOI] [PubMed] [Google Scholar]
  23. Uzan M., Leautey J., d'Aubenton-Carafa Y., Brody E. Identification and biosynthesis of the bacteriophage T4 mot regulatory protein. EMBO J. 1983;2(7):1207–1212. doi: 10.1002/j.1460-2075.1983.tb01568.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Uzan M., d'Aubenton-Carafa Y., Favre R., de Franciscis V., Brody E. The T4 mot protein functions as part of a pre-replicative DNA-protein complex. J Biol Chem. 1985 Jan 10;260(1):633–639. [PubMed] [Google Scholar]
  25. Wishart D. S., Sykes B. D., Richards F. M. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry. 1992 Feb 18;31(6):1647–1651. doi: 10.1021/bi00121a010. [DOI] [PubMed] [Google Scholar]
  26. de Franciscis V., Brody E. In vitro system for middle T4 RNA. I. Studies with Escherichia coli RNA polymerase. J Biol Chem. 1982 Apr 25;257(8):4087–4096. [PubMed] [Google Scholar]
  27. de Franciscis V., Favre R., Uzan M., Leautey J., Brody E. In vitro system for middle T4 RNA. II. Studies with T4-modified RNA polymerase. J Biol Chem. 1982 Apr 25;257(8):4097–4101. [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES