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Science 17 May 2002:
Vol. 296. no. 5571, pp. 1285 - 1290
DOI: 10.1126/science.1069595
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Research Articles

Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex

Katsuhiko S. Murakami, Shoko Masuda, Elizabeth A. Campbell, Oriana Muzzin, Seth A. Darst*

The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha 2beta beta 'omega sigma A) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma  subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma  subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.

The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
*   To whom correspondence should be addressed. E-mail: darst{at}rockefeller.edu

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