Repeated tertiary fold of RNA polymerase II and implications for DNA binding

Journal of Molecular Biology

Volumn 280, Issue 3, 1998, Pages 317-322

  Fu, Jianhua ^a   Gerstein, Mark ^a   David, Peter R ^a   Gnatt, Averell L ^a   Bushnell, David A ^a   Edwards, Aled M ^b   Kornberg, Roger D ^a  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

DNA binding; Folding; RNA polymerase II; Transcription; X ray diffraction

Indexed keywords

RNA POLYMERASE II;

ARTICLE; ENZYME SUBUNIT; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; YEAST;

EID: 0032540848     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1557     Document Type: Article

References (30)

1. Allison L.A., Moyle M., Shales M., Ingles C.J. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell. 42:1985;599-610
2. Bleasby A.J., Akrigg D., Attwood T.K. OWL a non-redundant composite protein sequence database. Nucl. Acids Res. 22:1994;3574-3577
3. Darst S.A., Edwards A.M., Kubalek E.W., Kornberg R.D. Three-dimensional structure of yeast RNA polymerase II at 16 Å resolution. Cell. 66:1991;121-128
4. Edwards A.M., Darst S.A., Feaver W.J., Thompson N.E., Burgess R.R., Kornberg R.D. Purification and lipid layer crystallization of yeast RNA polymerase II. Proc. Natl Acad. Sci. USA. 87:1990;2122-2126
5. Edwards A.M., Darst S.A., Hemming S.A., Li Y., Kornberg R.D. Epitaxial growth of protein crystals on lipid layers. Nature Struct. Biol. 1:1994;195-197
6. Fitzgerald P.M.D. MERLOT an integrated package of computer programs for the determination of crystal structures by molecular replacement. J. Appl. Crystallog. 21:1988;273-278
7. Garnier J., Gibrat J.F., Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266:1996;540-553
8. Kadesch T.R., Chamberlin M.J. Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template. J. Biol. Chem. 257:1982;5286-5295
9. Kerppola T.K., Kane C.M. Analysis of the signals for transcription termination by purified RNA polymerase II. Biochemistry. 29:1990;269-278
10. Landick R., Roberts J.W. The shrewd grasp of RNA polymerase. Science. 273:1996;202-203
11. Lee D.N., Phung L., Stewart J., Landick R. Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. J. Biol. Chem. 265:1990;15145-15153
12. Leuther K.K., Bushnell D.A., Kornberg R.D. Two-dimensional crystallography of transcription factor IIB- and IIE-RNA polymerase II complexes implications for start site selection and initiation complex formation. Cell. 85:1996;773-779
13. Matthews B.W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497
14. Navaza J. AMoRe an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163
15. Newman M., Strzelecka T., Dorner L.F., Schildkraut I., Aggarwal A.K. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature. 368:1994;660-664
16. Nudler E., Avetissova E., Markovtsov V., Goldfarb A. Transcription processivity protein-DNA interactions holding together the elongation complex. Science. 273:1996;211-217
17. Otwinowski Z. Oscillation data reduction program. Proceedings of the CCP4 Study Weekend Data Collection and Processing. 1993;56-62 SERC Daresbury Laboratory, Warrington WA4 4AD, UK
18. Pearson W.R., Lipman D.J. Improved tools for biological sequence analysis. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448
19. Pertoft H., Laurent T.C., Laas T. Density gradients prepared from colloidal silica. Anal. Biochem. 88:1978;. 271-182
20. Rees W., Keller R.W., Vesenka J.P., Yang G., Bustamante C. Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science. 260:1993;1646-1649
21. Rice G.A., Chamberlin J., Kane C.M. Contacts between mammalian RNA polymerase II and the template DNA in a ternary elongation complex. Nucl. Acids Res. 121:1993;113-118
22. Rossmann M.G., Blow D.M. The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallog. 15:1962;24-31
23. Rost B. PHD predicting one-dimensional protein secondary structure by profile-based neural networks. Methods Enzymol. 266:1996;525-539
24. Sweetser D., Nonet M., Young R.A. Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc. Natl Acad. Sci. USA. 84:1987;1192-1196
25. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W improving the sensibility of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680
26. Weilbaecher R., Hebron C., Feng G., Landick R. Termination-altering amino acid substitutions in the β′ subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation. Genes Dev. 8:1994;2913-2927
27. Westbrook E.M. Crystal density measurements using aqueous ficoll solutions. Methods Enzymol. 114:1985;187-196
28. Woychik N.A., Young R.A. RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth. Mol. Cell. Biol. 9:1989;2854-2859
29. Woychik N.A., Young R.A. RNA polymerase II subunit structure and function. Trends in Biochem. Sci. 15:1990;347-351
30. Young R.A. RNA polymerase II. Annu. Rev. Biochem. 60:1991;689-715