Transcriptional pausing by multisubunit RNA polymerases (RNAPs) is a key
mechanism for regulating gene expression in both prokaryotes and eukaryotes and
is a prerequisite for transcription termination. Pausing and termination states
are thought to arise through a common, elemental pause state that is inhibitory
for nucleotide addition. We report three crystal structures of Thermus RNAP
elemental paused elongation complexes (ePECs). The structures reveal the same
relaxed, open-clamp RNAP conformation in the ePEC that may arise by failure to
re-establish DNA contacts during translocation. A kinked bridge-helix sterically
blocks the RNAP active site, explaining how this conformation inhibits RNAP
catalytic activity. Our results provide a framework for understanding how RNA
hairpin formation stabilizes the paused state and how the ePEC intermediate
facilitates termination.
