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Structural basis of initial RNA polymerase II transcription.

Cheung AC, Sainsbury S, Cramer P
EMBO J 30 4755-63 (2011)
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Cited: 66 times
EuropePMC logo PMID: 22056778

Abstract

During transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II-DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3'-proximal phosphate of short RNAs. Short DNA-RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2'-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis.

Reviews - 4a3c mentioned but not cited (1)

  1. Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. Kaplan CD. Biochim. Biophys. Acta 1829 39-54 (2013)

Articles - 4a3c mentioned but not cited (2)

  1. Structural basis of initial RNA polymerase II transcription. Cheung AC, Sainsbury S, Cramer P. EMBO J 30 4755-4763 (2011)
  2. Genetic and structural study of DNA-directed RNA polymerase II of Trypanosoma brucei, towards the designing of novel antiparasitic agents. Papageorgiou L, Megalooikonomou V, Vlachakis D. PeerJ 5 e3061 (2017)


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