The structural changes of T7 RNA polymerase from transcription initiation to elongation

Current Opinion in Structural Biology

Volumn 19, Issue 6, 2009, Pages 683-690

  Steitz, Thomas A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; RNA POLYMERASE;

BASE PAIRING; BINDING SITE; CONFORMATIONAL TRANSITION; CROSS LINKING; DNA REPLICATION; DNA TEMPLATE; HETERODUPLEX ANALYSIS; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; RNA STRUCTURE; RNA SYNTHESIS; RNA TRANSCRIPTION; RNA TRANSLATION; RNA TRANSPORT; TRANSCRIPTION INITIATION;

DNA-DIRECTED RNA POLYMERASES; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 70549112913     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2009.09.001     Document Type: Review

References (22)

1. Cheetham G.M.T., and Steitz T.A. Structure of a transcribing T7 RNA polymerase initiation complex. Science 286 (1999) 2305
2. Yin Y.W., and Steitz T.A. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298 (2002) 1387
3. Tahirov T.H., Temiakov D., Anikin M., Patlan V., McAllister W.T., Vassylyev D.G., and Yokoyoma S. Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature 420 (2002) 43
4. Durniak K., Bailey S., and Steitz T.A. The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation. Science 322 (2008) 553-557. The crystal structures of T7 RNAP bound to substrate DNA and either a 7 nt or 8 nt transcript are described. They show a 40° and 45° rotation of the promoter binding domains resulting in an enlargement of the heteroduplex product binding cleft. They represent intermediate states in the transition from the initiation to elongation states.
5. Yin Y.W., and Steitz T.A. The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 116 (2004) 393
6. Berman A.J., Kamtekar S., Goodman S., Lázaro J.M., de Vega M., Blanco L., Salas M., and Steitz T.A. Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J 26 (2007) 3493-3505. These structures of ternary complex of phi29 DNA polymerase show conformational changes in the fingers domain of this B-family polymerase that are analogous to those of the A-family polymerases.
7. Brieba L.G., and Sousa R. T7 promoter release mediated by DNA scrunching. EMBO J 20 (2001) 6826
8. Cheetham G.M.T., Jeruzalmi D., and Steitz T.A. Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399 (1999) 80-83
9. Temiakov D., Mentesana P.E., Ma K., Mustaev A., Borukhov S., and McAllister W.T. The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance. Proc Natl Acad Sci U S A 97 (2000) 14109
10. Huang J., and Sousa R. T7 RNA polymerase elongation complex structure and movement. J Mol Biol 303 (2000) 347
11. Ma K., Temiakov D., Anikin M., and McAllister W.T. Probing conformational changes in T7 RNA polymerase during initiation and termination by using engineered disulfide crosslinks. Proc Natl Acad Sci U S A 102 (2005) 17612
12. Guo Q., and Sousa R. Translocation by T7 RNA polymerase: a sensitively poised Brownian ratchet. J Mol Biol 358 (2006) 241
13. Guillerez J., Lopez P.J., Proux F., Launay H., and Dreyfus M. A mutation in T7 RNA polymerase that facilitates promoter clearance. Proc Natl Acad Sci U S A 102 (2005) 5958
14. Temiakov D., Patlan V., Anikin M., McAllister M.T., Yokoyama S., and Vassylyev D.G. Structural basis for substrate selection by T7 RNA polymerases. Cell 116 (2004) 381
15. Doublié S.D., and Ellenberger T. The mechanism of action of T7 DNA polymerase. Curr Opin Struct Biol 8 (1998) 704
16. Doublié S., Tabor S., Long A.J., Richardson C.C., and Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391 (1998) 251
17. Li Y., Korolev S., and Waksman G. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J 17 (1998) 7514
18. Johnson S.J., Taylor J.S., and Beese L.S. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci U S A 100 (2003) 3895
19. Kiefer J.R., Mao C., Braman J.C., and Beese L.S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391 (1998) 304
20. Thomen P., Lopez P.J., and Heslot F. Unraveling the mechanism of RNA-polymerase forward motion by using mechanical force. Phys Rev Lett 94 (2005) 128102
21. Ideda R.A., and Richardson C.C. Interactions of a proteolytically nicked RNA polymerase of bacteriophage T7 with its promoter. J Biol Chem 262 (1987) 3800
22. Muller D.K., Martin C.T., and Coleman J.E. Processivity of proteolytically modified forms of T7 RNA polymerase. Biochemistry 27 (1988) 5763