1. Cellular Signaling Laboratory, RIKEN Harima Institute at Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
2. Structurome Research Group, RIKEN Harima Institute at Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
3. Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA
4. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
5. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

Correspondence to: Dmitry G. Vassylyev^1,2 Correspondence and requests for materials should be addressed to D.G.V. (e-mail: Email: dmitry@yumiyoshi.harima.riken.go.jp), S.Y. (e-mail: Email: yokoyama@biochem.s.u-tokyo.ac.jp) or S.B. (e-mail: Email: serbor@asan.com). The atomic coordinates have been deposited in the Protein Data Bank under accession number 1IW7.

Abstract

In bacteria, the binding of a single protein, the initiation factor , to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we report the crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 Å resolution. In the structure, two amino-terminal domains of the subunit form a V-shaped structure near the opening of the upstream DNA-binding channel of the active site cleft. The carboxy-terminal domain of is near the outlet of the RNA-exit channel, about 57 Å from the N-terminal domains. The extended linker domain forms a hairpin protruding into the active site cleft, then stretching through the RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.