Fig. 8: Interaction of the AR9 nvRNAP with DNA in the AR9 nvRNAP-Pro-Xray promoter complex.

a Atomic model of the AR9 nvRNAP promoter recognition element. Gp226 is shown as a semitransparent molecular surface. Only a small fragment of βN gp105 that participates in the formation of the ⁻¹⁰U binding pocket is shown for clarity. Interchain and DNA-intrachain hydrogen bonds are shown as dashed lines. Thin, straight lines connect the C5 atom of the uracil pyrimidine ring to the closest protein or DNA atoms that lie in-plane with the ring. The carbon atoms are colored as in Fig. 2a, except for V206, which is shown in cyan. b The in vitro transcription activity of the AR9 nvRNAP holoenzyme containing wild type (WT) gp226 or the V206G gp226 mutant has been tested using various U- and T-containing templates. c Interaction of the upstream oligonucleotide with the gp226 NTD. The same gp226 and βN gp105 fragments as in Fig. 8a are shown but are tilted to improve visibility. The nucleotides are numbered according to the original nomenclature of the template strand (Fig. 2b). The putative base identities and their numbers relative to the TSS (as would be found in a dsDNA transcription bubble) are given in midnight blue colored boxes. d The in vitro transcription activity of the AR9 nvRNAP holoenzyme containing gp226 mutants with an altered structure of the non-template strand binding groove. e, f The surface electrostatic potentials of the pseudo⁻³⁵-element binding motif in WT gp226 and the A⁵ gp226 mutant. g The ssDNA and dsDNA in vitro transcription activities of the AR9 nvRNAP holoenzyme containing WT gp226 and the A⁵ gp226 mutant. For each in vitro transcription experiment, two technical replicates of two biological replicates resulted in similar outcomes and one of them is shown. The uncropped autoradiographs are presented in Supplementary Fig. 1 and Supplementary Data 1.