The crystal structure of a hyperthermophilic archaeal TATA-box binding protein

Journal of Molecular Biology

Volumn 264, Issue 5, 1996, Pages 1072-1084

  DeDecker, Brian S ^a   O'Brien, Ronan ^b   Fleming, Patrick J ^a   Geiger, James H ^a   Jackson, Stephen P ^c   Sigler, Paul B ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Archaea; Structure; TBP; Thermophile; Transcription

Indexed keywords

BACTERIAL PROTEIN; DNA; TATA BINDING PROTEIN;

ARTICLE; BINDING AFFINITY; CALORIMETRY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIFFERENTIAL SCANNING CALORIMETRY; DISULFIDE BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN DNA BINDING; SEQUENCE HOMOLOGY; THERMOSTABILITY; X RAY DIFFRACTION;

EID: 0030596148     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0697     Document Type: Article

References (53)

1. Adams, M. W. W. (1993). Enzymes and proteins from organisms that grow near and above 100°C. Annu. Rev. Microbiol. 47, 627-658.
2. Barlow, D. J. & Thornton, J. M. (1983). Ion-pairs in proteins. J. Mol. Biol. 168, 867-885.
3. Brünger, A. T. (1992). The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-474.
4. Brünger, A. T. (1993). XPLOR Version 3.1: A System for X-ray Crystallography and NMR. Yale University Press, New Haven.
5. Bucher, P. (1990). Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212, 563-578.
6. Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., FitzGerald, L. M. & Clayton, R. A. (1996). Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science, 273(5278), 1058-1073.
7. Carson, M. (1991). Ribbons 2.0. J. Appl. Crystallog. 24, 958-961.
8. Chan, M. K., Mukund, S., Kietzin, A., Adams, M. W. W. & Rees, D. C. (1995). Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science, 267, 1463-1469.
9. Chasman, D. I., Flaherty, K. M., Sharp, P. A. & Kornberg, R. D. (1993). Crystal structure of yeast TATA-binding protein and model for interaction with DNA. Proc. Natl Acad. Sci. USA, 90, 8174-8178.
10. Coleman, R. A., Taggart, A. K. P., Benjamin, L. R. & Pugh, B. F. (1995). Dimerization of the TATA binding protein. J. Biol. Chem. 270, 13842-13849.
11. Connolly, M. L. (1985). Computation of molecular volume. J. Am. Chem. Soc. 107(5), 1118-1124.
12. Day, M. W., Hsu, B. T., Joshua-Tor, L., Park, J.-B., Zhou, Z. H., Adams, M. W. W. & Rees, D. C. (1992). X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci. 1, 1494-1507.
13. Dill, K. A. & Shortle, D. (1991). Denatured states of proteins. Annu. Rev. Biochem. 60, 795-825.
14. Forterre, P. (1996). A hot topic: the origin of hyperthermophiles. Cell 85, 789-792.
15. Geiger, J., Hahn, S., Lee, S. & Sigler, P. B. (1996). Crystal structure of the yeast TFIIA/TBP/DNA complex. Science, 272, 830-836.
16. Genetics Computer Group (1994). Wisconsin Package, 8th edit., Madison, Wisconsin.
17. Hahn, S., Buratowski, S., Sharp, P. A. & Guarente, L. (1989). Yeast TATA-binding protein binds to TATA elements with both consensus and nonconsensus DNA sequences. Proc. Natl Acad. Sci. USA, 86, 5718-5722.
18. Hennig, M., Darimont, B., Sterner, R., Kirschner, K. & Jansonius, J. N. (1995). 2.0 Å structure of indole-3-gycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinats of protein stability. Structure, 3, 1295-1306.
19. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A, 47, 110-119.
20. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
21. Kim, J. L., Nikolov, D. B. & Burley, S. K. (1993). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
22. Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature, 365(7), 512-520.
23. Korndörfer, I., Steipe, B., Huber, R., Tomschy, A. & Jaenicke, R. (1995). The crystal structure of hologlyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 Å resolution. J. Mol. Biol. 246, 511-521.
24. Kosa, P., Ghosh, G., DeDecker, B. S. & Sigler, P. B. (1996). Structural analysis of the TBP/TFIIB/DNA complex from the hyperthermophilic Archaea Pyrococcus woesei. Abstract no. 328. In Keystone Symposia (Transcriptional Mechanisms), Taos, New Mexico.
25. Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400.
26. Lee, W. S., Kao, C. C., Bryant, G. O., Liu, X. & Berk, A. J. (1991). Adenovirus E1A activation domain binds the basic repeat in the TATA box transcription factor. Cell, 67, 365-376.
27. Liu, X., Miller, C. W., Koeffler, P. H. & Berk, A. J. (1993). The p53 activation domain binds the TATA box-binding polypeptide in holo-TFIID, and a neighboring p53 domain inhibits transcription. Mol. Cell Biol. 13(6), 3291-3300.
28. Marsh, T. L., Reich, C. I., Whitelock, R. B. & Olsen, G. J. (1994). Transcription factor IID in the Archae: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes. Proc. Natl Acad. Sci. USA, 91, 4180-4184.
29. Miller, S., Janin, J., Lesk, A. M. & Chothia, C. (1987). Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-656.
30. Nicholls, A., Bharadwaj, R. & Honig, B. (1993). GRASP: graphical representation and analysis of surface properties. Biophys. J. 64, part 2, A166.
31. Nikolov, D. B. & Burley, S. K. (1994). 2.1 Å resolution refined structure of a TATA box-binding protein (TBP). Nature Struct. Biol. 1(9), 621-637.
32. Nikolov, D. B., Hu, S.-H., Lin, J., Gasch, A., Hoffmann, A., Horikoshi, M., Chua, N.-H., Roeder, R. G. & Burley, S. K. (1992). Crystal structure of TFIID TATA-box binding protein. Nature, 360, 40-46.
33. Nikolov, D. B., Chen, H., Halay, E. D., Usheva, A. A., Hisatake, K., Lee, D. K., Roeder, R. G. & Burley, S. K. (1995). Crystal structure of a TFIIB-TBP TATA-element ternary complex. Nature, 377, 119-128.
34. Otwinowski, Z. (1991). ML-PHARE CCP4 Proc 80-88, Daresbury Laboratory, Warrington, UK.
35. Otwinowski, Z. (1993). In Data Collection and Processing, Warrington, England.
36. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. (1995). How to measure and predict the molar adsorption coefficient of a protein. Protein Sci. 4, 2411-2423.
37. Palmer, J. R. & Daniels, C. J. (1995). In vivo definition of an archaeal promoter. J. Bacteriol. 177(7), 1844-1849.
38. Pattabiraman, N., Ward, K. B. & Fleming, P. J. (1995). Occluded molecular surface: analysis of protein packing. J. Mol. Recognit. 8, 334-344.
39. Petri, V., Hsieh, M. & Brenowitz, M. (1995). Thermodynamic and kinetic characterization of the binding of the TATA binding protein to the adenovirus E4 promoter. Biochemistry, 34(31), 9977-9984.
40. Privalov, P. L. (1980). Scanning microcalorimeters for studying macromolecules. Pure Appl. Chem. 52, 479-497.
41. Qureshi, S. A., Baumann, P., Rowlands, T., Khoo, B. & Jackson, S. P. (1995a). Cloning and functional analysis of the TATA binding protein from Sulfolobus shibatae. Nucl. Acids Res. 23(10), 1775-1781.
42. Qureshi, S. A., Khoo, B., Baumann, P. & Jackson, S. P. (1995b). Molecular cloning of the transcription factor TFIIB homolog from Sulfolobus shibatae. Proc. Natl Acad. Sci USA, 92, 6077-6081.
43. Rashin, A. A., Iofin, M. & Honig, B. (1986). Internal cavities and buried waters in globular proteins. Biochemistry, 25(12), 3619-3625.
44. Richards, F. M. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14.
45. Richards, F. M. & Lim, W. A. (1994). An analysis of packing in the protein folding problem. Quart. Rev. Biophys. 26(4), 423-498.
46. Rowlands, T., Baumann, P. & Jackson, S. P. (1994). The TATA-binding protein: a general transcription factor in eukaryotes and Archaebacteria. Science, 264, 1326-1329.
47. Scholz, S., Sonnenbichler, J., Schäfer, W. & Hensel, R. (1992). Di-myo-inositol-1,1′-phosphate: a new inositol phosphate isolated from Pyrococcus woesei. FEBS Letters, 306(2,3), 239-242.
48. Sheldrick, G. M. (1990). Phase annealing in Shelx-90: direct methods for larger structures. Acta Crystallog. 46, 467-473.
49. Tan, S., Hunziker, Y., Sargent, D. F. & Richmond, T. J. (1996). Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature, 381, 127-134.
50. Woese, C. R. (1987). Bacterial evolution. Microbiol. Rev. 221-271.
51. Woese, C. R., Kandler, O. & Wheelis, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archae, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA, 87, 4576-4579.
52. Yip, K. S. P., Stillman, T. J., Britton, K. L., Artymiuk, P. J., Baker, P. J., Sedelnikova, S. E., Engel, P. C., Pasquo, A., Chiaraluce, R., Consalvi, V., Scandurra, R. & Rice, D. W. (1995). The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure, 3, 1147-1158.
53. Zillig, W., Palm, P., Klenk, H.-P., Langer, D., Hüdepohl, U., Hain, J., Lanzendörfer, M. & Holz, I. (1993). Transcription in archaea. In The Biochemistry of Archaea (Archaebacteria) (Kates, M., Kushner, D. J. & Matheson, A. T., eds), vol. 26, pp. 367-386, Elsevier, Amsterdam.