InterPro : IPR013324

Name  RNA polymerase sigma factor, region 3/4 Short Name  RNA_pol_sigma_r3_r4
Type  Domain Description  The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents regions 3 and 4 (or sigma3 and sigma4 domains) found in several sigma factors, often in conjunction with the sigma2 domain (). Both regions are present in Sigma70 [], Sigma28 (FliA), and SigA [], while region4 is also found in SigmaF []and RpoE. Both regions 3 and 4 have a nucleotide-binding 3-helical core structure, consisting of a closed or partly open bundle with a right-handed twist. Some other nucleotide-binding proteins are thought to contain domains with a similar topology.

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



1 Child Features

Id Name Short Name Type
IPR013249 RNA polymerase sigma factor 70, region 4 type 2 RNA_pol_sigma70_r4_t2 Domain

2 Contains

Id Name Short Name Type
IPR007630 RNA polymerase sigma-70 region 4 RNA_pol_sigma70_r4 Domain
IPR007624 RNA polymerase sigma-70 region 3 RNA_pol_sigma70_r3 Domain

20 Found In

Id Name Short Name Type
IPR011991 Winged helix-turn-helix DNA-binding domain WHTH_DNA-bd_dom Domain
IPR014284 RNA polymerase sigma-70 like domain RNA_pol_sigma-70_dom Domain
IPR000943 RNA polymerase sigma-70 RNA_pol_sigma70 Domain
IPR012759 RNA polymerase sigma factor RpoH, proteobacteria RNA_pol_sigma_RpoH_proteobac Family
IPR014200 RNA polymerase sigma-E type RNA_pol_sigma-E Family
IPR014209 RNA polymerase sigma-K type RNA_pol_sigma-K Family
IPR016262 RNA polymerase sigma factor, SigB/SigC/SigD, plastid RNA_pol_sigma_SigB/C/D_plastid Family
IPR012845 RNA polymerase sigma factor, FliA/WhiG RNA_pol_sigma_FliA_WhiG Family
IPR014305 RNA polymerase sigma-G type, actinobacteria RNA_pol_sigma-G_actinobac Family
IPR014322 RNA polymerase sigma-B/F/G type RNA_pol_sigma-B/F/G Family
IPR014212 RNA polymerase sigma-G type RNA_pol_sigma-G Family
IPR014236 RNA polymerase sigma-F type RNA_pol_sigma-F Family
IPR014288 RNA polymerase sigma-B factor RNA_pol_sigma-B Family
IPR014300 RNA polymerase sigma-V type RNA_pol_sigma-V Family
IPR014294 RNA polymerase sigma-W, bacillaceae RNA_pol_sigma-W_bacilli Family
IPR011517 RNA polymerase sigma-70 ECF-like RNA_pol_sigma70_ECF-like Family
IPR012760 RNA polymerase sigma factor RpoD, C-terminal RNA_pol_sigma_RpoD_C Domain
IPR012761 RNApolymerase sigma factor RpoS RNA_pol_sigma_RpoS Family
IPR017848 RNA polymerase sigma factor, RpoD-like, cyanobacteria RNA_pol_sigma_RpoD_cyanobac Family
IPR007394 Putative helix-turn-helix protein, YlxM/p13-like UPF0122 Family

0 Parent Features

6 Publications

First Author Title Year Journal Volume Pages
Helmann JD Structure and function of bacterial sigma factors. 1988 Annu Rev Biochem 57 839-72
Lonetto M The sigma 70 family: sequence conservation and evolutionary relationships. 1992 J Bacteriol 174 3843-9
Gribskov M Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. 1986 Nucleic Acids Res 14 6745-63
Campbell EA Structure of the bacterial RNA polymerase promoter specificity sigma subunit. 2002 Mol Cell 9 527-39
Malhotra A Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. 1996 Cell 87 127-36
Campbell EA Crystal structure of the Bacillus stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor sigmaF. 2002 Cell 108 795-807

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)