Fig. 2: DNA upstream fork promoter binds to Msm HelD–σA–RbpA–RNAP complex.
From: Mycobacterial HelD connects RNA polymerase recycling with transcription initiation
a Sequence of the us-fork promoter DNA fragment. The numbers above denote the DNA position with respect to the transcription start site (+1). The −35 and −10 elements are colored yellow, nt/t denotes non-template/template strand, respectively. b–d Three conformations of the Msm RNAP core complex together with us-fork promoter DNA fragment, σA, RbpA, and HelD. One conformation is in state II (us-fork-HelD–RPc-II) and two conformations are in state III (us-fork–HelD–RPc-III, us-fork–HelDN-term–RPc-III), respectively. In us-fork–HelD–RPc-II, the whole HelD protein is ordered on RNAP, in us-fork–HelD–RPc-III the 1A–2A NTPase is disengaged and thus HelD–CO tilts relative to the primary channel. In us-fork-HelDN-term-RPc-III, only the HelDN-term domain is bound in the secondary channel and the rest of the HelD protein is not ordered. Individual domains are color-coded as defined in Fig. 1d. e–g Close-up views of the RNAP primary channel, corresponding to panels (b–d), respectively. The black scale bar illustrates the distance between the β-lobe and the N-terminus of the σA2 domain, which directly correlates with the primary channel closure according to Supplementary Table 3. e Presence of HelD–CO (light blue) keeps the RNAP primary channel wide open. The σAN-helix wraps specifically around the HelD–CO-tip. f Tilting (compare HelD–CO axes) of HelD–CO disfavors CO-tip interaction with the σA2 domain and prevents CO-tip interaction with the σAN-helix. g Displacement of all HelD domains, except for HelDN-term(as depicted in d), allows a partial closure of the RNAP primary channel but not to the extent that would allow the σAN-helix interaction with the β-lobe as seen in the σA–RbpA–RNAP complex (Supplementary Fig. 8d).
