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Architecture of initiation-competent 12-subunit RNA polymerase II
- Institute of Biochemistry and Gene Center, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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Edited by E. Peter Geiduschek, University of California at San Diego, La Jolla, CA, and approved March 27, 2003 (received for review January 31, 2003)
Abstract
RNA polymerase (Pol) II consists of a 10-polypeptide catalytic core and the two-subunit Rpb4/7 complex that is required for transcription initiation. Previous structures of the Pol II core revealed a “clamp,” which binds the DNA template strand via three “switch regions,” and a flexible “linker” to the C-terminal repeat domain (CTD). Here we derived a model of the complete Pol II by fitting structures of the core and Rpb4/7 to a 4.2-Å crystallographic electron density map. Rpb4/7 protrudes from the polymerase “upstream face,” on which initiation factors assemble for promoter DNA loading. Rpb7 forms a wedge between the clamp and the linker, restricting the clamp to a closed position. The wedge allosterically prevents entry of the promoter DNA duplex into the active center cleft and induces in two switch regions a conformation poised for template-strand binding. Interaction of Rpb4/7 with the linker explains Rpb4-mediated recruitment of the CTD phosphatase to the CTD during Pol II recycling. The core–Rpb7 interaction and some functions of Rpb4/7 are apparently conserved in all eukaryotic and archaeal RNA polymerases but not in the bacterial enzyme.
Footnotes
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↵ * To whom correspondence should be addressed. E-mail: cramer{at}LMB.uni-muenchen.de.
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This paper was submitted directly (Track II) to the PNAS office.
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Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID code 1NT9).
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Abbreviations: Pol, RNA polymerase; CTD, C-terminal repeat domain.
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See commentary on page 6893.
- Copyright © 2003, The National Academy of Sciences
