Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).
Comment:based on the binding of E. coli sigmaE SR4 and T. aquaticus sigmaA SR4 to their -35 elements. These proteins use distinct mechanisms. E. coli sigmaE SR4 binds 4 A further into the major groove than the latter, making more extensive contacts. It also recognizes a different -35 consensus sequence than that of Thermus aquaticus sigmaA.
Structure:2H27_A, Escherichia coli sigmaE SR4 bound to its -35 element 7-base-pair consensus GGAACTT DNA, contacts at 3.5 A. - View structure with Cn3D
Structure:1L9Z_H, Thermus aquaticus RNA polymerase holoenzyme/ FORK-Junction promoter complex, showing sigmaA bound with a promoter DNA fragment, contacts at 3.5A. - View structure with Cn3D
Lu S et al.(2020). "CDD/SPARCLE: the conserved domain database in 2020.",