The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase

Current Opinion in Structural Biology

Volumn 14, Issue 1, 2004, Pages 4-9

  Steitz, Thomas A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

DNA polymerase; DNAP; NTP; Nucleoside 5 triphosphate; PPi; Pyrophosphate; RNA polymerase; RNAP

Indexed keywords

DOUBLE STRANDED DNA; RNA POLYMERASE;

AMINO TERMINAL SEQUENCE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA DETERMINATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN CONFORMATION; PROTEIN DOMAIN; REVIEW; RNA TRANSCRIPTION; RNA TRANSLATION; RNA TRANSPORT; TRANSCRIPTION INITIATION;

EID: 1342302799     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2004.01.006     Document Type: Review

References (18)

1. von Hippel P.H., Bear D.G., Morgan W.D., McSwiggen J.A. Protein-nucleic acid interactions in transcription: a molecular analysis. Annu. Rev. Biochem. 53:1984;389-446.
2. von Hippel P.H. An integrated model of the transcription complex in elongation, termination, and editing. Science. 281:1998;660-665.
3. Carpousis A.J., Gralla J.D. Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter. Biochemistry. 19:1980;3245-3253.
4. Martin C.T., Muller D.K., Coleman J.E. Processivity in early stages of transcription by T7 RNA polymerase. Biochemistry. 27:1988;3966-3974.
5. Cheetham G.M.T., Steitz T.A. Structure of a transcribing T7 RNA polymerase initiation complex. Science. 286:1999;2305-2309.
6. Yin Y.W., Steitz T.A. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science. 298:2002;1387-1395 This paper compares structures of the initiation complex [5] with that of the elongation complex, and provides the basis for understanding promoter clearance and the processivity of the elongation complex.
7. Tahirov T.H., Temiakov D., Patlan A.M., McAllister W.T., Vassylyev D.G., Yokoyama S. Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature. 420:2002;43-50 The structure of an elongation complex is presented and its relationship to the initiation complex [5] discussed.
8. Krakow J.S., Fronk E. Azotobacter vinelandii ribonucleic acid polymerase. 8. Pyrophosphate exchange. J. Biol. Chem. 244:1969;5988-5993.
9. Yin YW, Steitz TA: The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 2004, in press.
10. He B., Rong M., Durbin W.T., McAllister J. A mutant T7 RNA polymerase that is defective in RNA binding and blocked in the early stages of transcription. J. Mol. Biol. 265:1997;275-288.
11. Kuriyan J., O'Donnell M. Sliding clamps of DNA polymerases. J. Mol. Biol. 234:1993;915-925.
12. Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science. 292:2001;1876-1882 The structure of yeast RNA polymerase II bound to an elongation phase substrate containing downstream duplex DNA and RNA paired with a template extension is described. A proposal for translocation is presented.
13. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution. Science. 292:2001;1863-1876 The structure of an elongation complex of yeast RNA polymerase II is presented.
14. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell. 98:1999;811-824.
15. Murakami K.S., Masuda S., Campbell E.A., Mussin O., Darst S.A. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science. 296:2002;1285-1290.
16. Doublié S., Ellenberger T. The mechanism of action of T7 DNA polymerase. Curr. Opin. Struct. Biol. 8:1998;704-712.
17. Pelletier H., Sawaya M.R., Wolfie W., Wilson S.H., Kraut J. Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity and fidelity. Biochemistry. 35:1996;12742-12761.
18. Johnson S.J., Taylor J.S., 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;3895-3900.