X-ray crystallographic studies of eukaryotic transcription factors

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 63, Issue , 1998, Pages 33-40

  Burley, S K ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE NUCLEOTIDE EXCHANGE FACTOR; HISTONE; RNA POLYMERASE; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR; CURVED DNA; DNA DIRECTED RNA POLYMERASE; HETERODIMER; INITIATION FACTOR; TATA BINDING PROTEIN RELATED FACTOR; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR;

ARABIDOPSIS; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIMERIZATION; DNA HISTONE INTERACTION; EUKARYOTE; GENETIC TRANSCRIPTION; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN TERTIARY STRUCTURE; STEREOCHEMISTRY; TATA BOX; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; X RAY CRYSTALLOGRAPHY; CARBOXY TERMINAL SEQUENCE; DNA BINDING; DNA PACKAGING; GENE DUPLICATION; GENE EXPRESSION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; PROMOTER REGION; PROTEIN CONFORMATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; THREE DIMENSIONAL IMAGING;

EID: 0032467007     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.1998.63.33     Document Type: Conference Paper

References (53)

1. Arents G. and Moudrianakis E. 1993. Topography of the histone octamer surface: Repeating structural motifs utilized in the docking of nucleosomal DNA. Proc. Natl. Acad. Sci. 90: 10489.
2. _. 1995. The histone fold: A ubiquitous architectural motif utilized in DNA compaction and protein dimerization. Proc. Natl. Acad. Sci. 92: 11170.
3. Arents G., Burlingame R.W., Wang B.-C., Love W.E., and Moudrianakis E.N. 1991. The nucleosomal core histone octamer at 3.1Å resolution: A tripartite protein assembly and a left-handed superhelix. Proc. Natl. Acad. Sci. 88: 10148.
4. Bagby S., Kim S., Maldonado E., Tong K., Reinberg D., and Ikura M. 1995. Solution structure of the C-terminal core domain of human TFIIB: Similarity to cyclin A and interaction with TATA-binding protein. Cell 82: 857.
5. Baxevanis A., Arents G., Moudrianakis E., and Landsman D. 1995. A variety of DNA-binding and multimeric proteins contain the histone fold motif. Nucleic Acids Res. 23: 2685.
6. Buratowski S., Hahn S., Guarente L., and Sharp P.A. 1989. Five intermediae complexes in transcription initiation by RNA polymerase II. Cell 56: 549.
7. Burley S.K. and Roeder R.G. 1996. Biochemistry and structural biology of transcription factor IID. Annu. Rev. Biochem. 65: 769.
8. Chasman D., Flaherty K., Sharp P.A., and Kornberg R. 1993. Crystal structure of yeast TATA-binding protein and a model for interaction with DNA. Proc. Natl. Acad. Sci. 90: 8174.
9. Clark K.L., Halay E.D., Lai E., and Burley S.K. 1993. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature 364: 412.
10. Coleman R. and Pugh B.F. 1995. Evidence for functional binding and stable sliding of the TATA binding protein on non-specific DNA. J. Biol. Chem. 270: 13850.
11. Coleman R., Taggart A., Benjamin L., and Pugh B. 1995. Dimerization of TATA binding protein. J. Biol. Chem. 270: 13842.
12. Comai L., Tanese N., and Tjian R. 1992. The TATA-binding protein and associated factors are integral components of RNA polymerase I transcription factor, SL1. Cell 68: 965.
13. Gabrielson O. and Sentenac A. 1991. RNA polymerase III (C) and its transcription factors. Trends Biochem. Sci. 16: 412.
14. Hernandez N. 1993. TBP, a universal transcription factor? Genes Dev. 7: 1291.
15. Hisatake K., Ohta T., Takada R., Guermah M., Horikoshi M., Nakatani Y., and Roeder R.G. 1995. Evolutionary conservation of human TBP-associated factors TAF31 and TAF80 and interactions of TAF80 with other TAFs and with general transcription factors. Proc. Natl. Acad. Sci. 92: 8195.
16. Hoffmann A., Chiang C.-M., Oelgeschlager T., Xie X., Burley S.K., Nakatani Y., and Roeder R.G. 1996. A histone octamer-like structure within TFIID. Nature 380: 356.
17. Hoopes B., LeBlanc J., and Hawley D. 1992. Kinetic analysis of yeast TFIID-TATA box complex formation suggests a multi-step pathway. J. Biol. Chem. 267: 11539.
18. Hori R. and Carey M. 1994. The role of activators in assembly of RNA polymerase II transcription complexes. Curr. Opin. Genet. Dev. 4: 236.
19. Janin J. 1995. Elusive affinities. Proteins 21: 30.
20. Jeffrey P., Russo A., Polyak K., Gibbs E., Hurwitz J., Massague J., and Pavletich N. 1995. Mechanism of CDK activation revealed by the structure of a cyclin A-CDK2 complex. Nature 376: 313.
21. Karantza V., Friere E., and Moudrianakis E. 1996. Thermodynamic studies of the core histones: pH and ionic strength effects on the stability of the (H3-H4)/(H3-H4)2 system. Biochemistry 35: 2037.
22. Kim J.L. and Burley S.K. 1994. 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat. Struct. Biol. 1: 638.
23. Kim J.L., Nikolov D.B., and Burley S.K. 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365: 520.
24. Kim Y., Geiger J.H., Hahn S., and Sigler P.B. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365: 512.
25. Klug A., Rhodes D., Smith J., Finch J.T., and Thomas J.O. 1980. A low resolution structure for the histone core of the nucleosome. Nature 287: 509.
26. Kokubo T., Gong D.-W., Wootton J., Horikoshi M., Roeder R.G., and Nakatani Y. 1994. Molecular cloning of Drosophila TFIID subunits. Nature 367: 484.
27. Koleske A. and Young R. 1995. The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem. Sci. 20: 113.
28. Kraulis P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946.
29. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. 1997. Crystal structure of the nucleosome core particle at 2.8Å resolution. Nature 389: 251.
30. Maldonado E. and Reinberg D. 1995. News on initiation and elongation of transcription by RNA polymerase II. Curr. Opin. Cell Biol. 7: 352.
31. Matsui T., Segall J., Weil P., and Roeder R.G. 1980. Multiple factors required for accurate initiation of transcription by purified RNA polymerase II. J. Biol. Chem. 255: 11992.
32. McPherson C., Shin E.-Y., Friedman D., and Zaret K. 1993. An acitve tissue-specific enhancer and bound transcription factors existing in a precisely position nucleosomal array. Cell 75: 387.
33. Mengus G., May M., Jacq X., Staub A., Tora L., Chambon P., and Davidson I. 1995. Cloning and characterization of hTAFII18, hTAFII20 and hTAFII28: Three subunits of the human transcription factor TFIID. EMBO J. 14: 1520.
34. Nikolov D.B. and Burley S.K. 1994. 2.1Å resolution refined structure of a TATA box-binding protein (TBP). Nat. Struct. Biol. 1: 621.
35. Nikolov D.B., Chen H., Malay E.D., Hoffmann A., Roeder R.G., and Burley S.K. 1996. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl. Acad. Sci. 93: 4956.
36. Nikolov D.B., Chen H., Halay E., Usheva A., Hisatake K., Lee D., Roeder R.G., and Burley S.K. 1995. Crystal structure of a TFIIB-TBP-TATA element ternary complex. Nature 377: 119.
37. Nikolov D.B., Hu S.-H., Lin J., Gasch A., Hoffmann A., Horikoshi M., Chua N.-H., Roeder R.G., and Burley S.K. 1992. Crystal structure of TFIID TATA-box binding protein. Nature 360: 40.
38. Parkhurst K., Brenowitz M., and Parkhurst L. 1996. Simultaneous binding and bending of promoter DNA by TBP: Real time kinetic measurements. Biochemistry 35: 7459.
39. Parvin J. and Sharp P. 1993. DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 73: 533.
40. Parvin J., McCormick R., Sharp P., and Fisher D. 1995. Prebending of a promoter sequence enhances affinity for the TATA-binding factor. Nature 273: 724.
41. Perez-Howard G., Weil P., and Beechem J. 1995. Yeast TATA binding protein interaction with DNA: Fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics. Biochemistry 34: 8005.
42. Pruss D., Hayes J., and Wolffe A. 1995. Nucleosomal anatomy-where are the histones? BioEssays 17: 161.
43. Ramakrishnan V., Finch J., Graziano V., and Sweet R.M. 1993. Crystal structure of the globular domain of histone H5 and its implications for nucleosome binding. Nature 362: 219.
44. Reeder R. 1992. Regulation of transcription by RNA polymerase I. In Transcriptional regulation (ed. S. McKnight and K.R. Yamamoto), p. 315. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
45. Roeder R.G. 1991. The complexities of eukaryotic transcription initiation: Regulation of preinitiation complex assembly. Trends Biochem, Sci. 16: 402.
46. Sentenac A. 1985. Eukaryotic RNA polymerases. CRC Crit. Rev. Biochem. 18: 31.
47. Starr D., Hoopes B., and Hawley D. 1995. DNA bending is an important component of site-specific recognition by the TATA binding protein. J. Mol. Biol. 250: 434.
48. Sun D. and Hurley L. 1995. TBP unwinding of the TATA box induces a specific downstream unwinding site that is targeted by pluramycin. Chem. Biol. 2: 457.
49. Wang Z. and Roeder R.G. 1995. Structure and function of a human transcription factor TFIIIB subunit that is evolutionarily conserved and contains both TFIIB- and high-mobility-group protein 2 domains. Proc. Natl. Acad. Sci. 92: 7026.
50. Wong J. and Bateman E. 1994. TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs. Nucleic Acids Res. 22: 1890.
51. Xie X., Kokubo T., Cohen S.L., Hoffmann A., Chait B.T., Roeder R.G., Nakatani Y., and Burley S.K. 1996. Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature 380: 316.
52. Zawel L. and Reinberg D. 1993. Initiation of transcription by RNA polymerase II: A multi-step process. Prog. Nucleic Acid Res. Mol. Biol. 44: 67.
53. Zawel L., Kumar K., and Reinberg D. 1995. Recycling of the general transcription factors during RNA polymerase II transcription. Genes Dev. 9: 1479.