Fig. 6: HelD participates during transcription initiation.
From: Mycobacterial HelD connects RNA polymerase recycling with transcription initiation
The circular arrangement model of HelD participation in transcription initiation is only the best approximation of the event succession displayed in panels a–g: a HelD binds to the RNAP core together with σA and RbpA. Individual domains are color-coded according to the legend above. The HelD CO-domain interacts with σA2 and σAN-helix in the context of β′-clamp. In State I, the presence of full-length HelD in the primary channel (PCh) makes the β′-clamp wide open. However, it does not interfere with the AS and the RIF binding pocket. b In State II, the RNAP β′-clamp is maximally open and the HelD PCh-loop reaches the RNAP AS cavity and interferes with the RIF binding pocket. Concomitantly, in State II, the HelD–σA–RbpA–RNAP complex is able to recognize and bind DNA promoter outside the primary channel. c Disengagement of the HelD NTPase domain loosens the grip of the CO domain on the β′-clamp, the consequent narrowing of the primary channel tilts the CO domain. Still, the PCh-loop tip is folded into to AS cavity and interferes with the RIF binding pocket. d HelD clearance from the primary channel allows for β′-clamp closing, however HelDN-term presence in the secondary channel restricts the full closure. e Partial loading of dwDNA is compatible with HelD binding to the secondary channel, however, further interaction of dwDNA within the RNAP primary channel (f) triggers a conformational change of the secondary channel which disfavors and expels HelDN-term. σAN-helix helps to accommodate dwDNA towards the RP2-like intermediate. g In order to establish the RNAP open complex (competent for the first cycle of nucleotide addition), the DNA promoter still needs to be further accommodated into the RNAP AS cavity. At that moment, RNAP clamps around the dwDNA and σAN-helix locks the clamp by interaction with the β-lobe. From this state the complex can proceed towards transcription initiation or, when stalled by RIF, reverse towards HelD–RPc (gray dashed line arrow).
