title: Structural basis of initial RNA polymerase II transcription.
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.
authors: Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany.
authors: Alan C M
authors: AC
authors: Cheung
authors: Sarah
authors: S
authors: Sainsbury
authors: Patrick
authors: P
authors: Cramer
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D008958:Models, Molecular; D009711:Nucleotides / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism; D012319:RNA Polymerase II / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D014158:Transcription, Genetic / Q000502:physiology*; D035602:Transcriptional Elongation Factors / Q000378:metabolism
chemical_list: D009711:Nucleotides; D035602:Transcriptional Elongation Factors; D012313:RNA; D004247:DNA; D012319:RNA Polymerase II; D008239:Lysine