Fig. 3: HelD release on the pathway towards RPo complex formation.
From: Mycobacterial HelD connects RNA polymerase recycling with transcription initiation
a Sequence of the promoter transcription bubble DNA fragment. The numbers above denote the DNA position with respect to the TSS (+1). The −35 and −10 elements are colored yellow; nt/t denotes non-template/template strand, respectively. b Msm RNAP core complex together with the promoter transcription bubble DNA fragment, σA, RbpA and HelD in the RP2 like-state (HelDN-term–RP2). Only the HelDN-term domain is present in the secondary channel, the rest of the HelD protein is not ordered. The dwDNA is partially loaded into the primary channel. Individual domains are color-coded as in Fig. 1d. c, d Msm RNAP core complex together with the promoter transcription bubble DNA fragment, σA, RbpA, (no HelD), in the RP2-like state (σAN-helix–RP2) and Mtb RP2 RNAP complex (RP2 promoter–DNA–σA–RNAP) PDB 6EE8, respectively. Individual domains are color-coded as in Fig. 1d, CarD in panel d is transparent green. e–g Close-up views of the RNAP primary channel from 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 The presence of HelDN-term (firebrick) in the secondary channel prevents the RNAP primary channel from closing completely. Concomitantly, dwDNA is only partially loaded into the primary channel. f Displacement of the HelDN-term domain is followed by a slight adjustment of the RNAP primary channel and interaction of σAN-helix with the dwDNA. g In the RP2 complex (PDB 6EE8), the RNAP primary channel closes around dwDNA so that the σAN-helix directly interacts with the β-lobe domain. CarD interacts with the −10 element and stabilizes the transcription bubble.
