Averell L. Gnatt,* Patrick Cramer 1, Jianhua Fu 2, David A. Bushnell, Roger D. Kornberg§
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
*Present address: Department of Pharmacology and Experimental Therapy,
University of Maryland, 655 West Baltimore Street, HH403, Baltimore, MD
21201, USA.
1 Present address: Institute of Biochemistry, Gene Center,
University of Munich, 81377 Munich, Germany.
2 Present address: Department of Molecular Biology and
Genetics, Cornell University, 223 Biotechnology Building, Ithaca, NY 14853,
USA.
§ To whom correspondence should be addressed. E-mail: kornberg@stanford.edu
Summary:
The crystal structure of RNA polymerase II in the act of transcription
was determined at 3.3 Å resolution. Duplex DNA is seen entering the
main cleft of the enzyme and unwinding before the active site. Nine base
pairs of DNA-RNA hybrid extend from the active center at nearly right angles
to the entering DNA, with the 3' end of the RNA in the nucleotide addition
site. The 3' end is positioned above a pore, through which nucleotides
may enter and through which RNA may be extruded during back-tracking. The
5'-most residue of the RNA is close to the point of entry to an exit groove.
Changes in protein structure between the transcribing complex and free
enzyme include closure of a clamp over the DNA and RNA and ordering of
a series of "switches" at the base of the clamp to create a binding site
complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help
explain DNA and RNA strand separation, the specificity of RNA synthesis,
"abortive cycling" during transcription initiation, and RNA and DNA translocation
during transcription elongation.
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RNA Polymerase II at 2.8
Ångstrom Resolution", Science vol.
292: pp. 1863-1876 (June 8, 2001).
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Interaction",
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2000).
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Chromatin by Nuclear RNA Species",
"RNA 2001", page 237 (May 30, 2001).