InterPro : IPR007627

Name  RNA polymerase sigma-70 region 2 Short Name  RNA_pol_sigma70_r2
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 [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].
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Sequence Features

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Proteins

InterPro protein domain ID --> Contigs

 

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0 Child Features

1 Contains

Id Name Short Name Type
IPR000838 RNA polymerase sigma factor 70, ECF, conserved site RNA_pol_sigma70_ECF_CS Conserved_site

32 Found In

Id Name Short Name Type
IPR013325 RNA polymerase sigma factor, region 2 RNA_pol_sigma_r2 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
IPR016371 RNA polymerase sigma-H factor RNA_pol_sigma-H_factor Family
IPR014218 RNA polymerase sigma-H type RNA_pol_sigma-H Family
IPR016263 RNA polymerase sporulation-specific sigma factor, SigK/SigE RNA_pol_sigma-SigE/K 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
IPR014327 RNA polymerase sigma-70, Bacteroidetes type RNA_pol_sigma70_bacteroid Family
IPR014325 RNA polymerase sigma-E type, actinobacteria RNA_pol_sigma-E_actinobac Family
IPR014326 RNA polymerase sigma-70 factor, Planctomycetaceae RNA_pol_sigma-70_Plancto 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
IPR014331 RNA polymerase sigma-70 ECF-like, Rhodopirellula baltica RNA_pol_sigma70_ECF_RHOBA Family
IPR014303 RNA polymerase sigma-70, ECF type RNA_pol_sigma-70_ECF Family
IPR014304 RNA polymerase sigma-Z type RNA_pol_sigma-Z Family
IPR014300 RNA polymerase sigma-V type RNA_pol_sigma-V Family
IPR014244 RNA polymerase sigma-I type RNA_pol_sigma-I Family
IPR014289 RNA polymerase sigma-24-related RNA_pol_sigma-24-rel Family
IPR014286 RNA polymerase sigma-70 RpoE type RNA_pol_sigma70_RpoE Family
IPR014296 RNA polymerase sigma-M, bacillaceae RNA_pol_sigma-M_bacilli Family
IPR014293 RNA polymerase sigma-70, actinobacteria RNA_pol_sigma70_actinobac Family
IPR014298 RNA polymerase sigma-X type RNA_pol_sigma-X Family
IPR012760 RNA polymerase sigma factor RpoD, C-terminal RNA_pol_sigma_RpoD_C Domain

0 Parent Features

5 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



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)