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Abstract:
The crystal structure of RNA polymerase II in the act of transcription was
determined at 3.3 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 39 end of the RNA in the nucleotide addition site. The 39 end is
positioned above a pore, through which nucleotides may enter and through
which RNA may be extruded during back-tracking. The 59-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 ÒswitchesÓ at the base of the
clamp to create a binding site complementary to the DNA-RNA hybrid. ProteinÐ
nucleic acid contacts help explain DNA and RNA strand separation, the speci
Þcity of RNA synthesis, Òabortive cyclingÓ during transcription initiation, and
RNA and DNA translocation during transcription elongation.
