Protein Domain : IPR012760

Type:  Domain Name:  RNA polymerase sigma factor RpoD, C-terminal
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 the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. 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 [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Short Name:  RNA_pol_sigma_RpoD_C
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0 Child Features

5 Contains

DB identifier Type Name
IPR011991 Domain Winged helix-turn-helix DNA-binding domain
IPR013324 Domain RNA polymerase sigma factor, region 3/4
IPR007627 Domain RNA polymerase sigma-70 region 2
IPR007630 Domain RNA polymerase sigma-70 region 4
IPR007624 Domain RNA polymerase sigma-70 region 3

1 Cross References

Identifier
TIGR02393

0 Found In

4 GO Annotations

GO Term Gene Name
GO:0003677 IPR012760
GO:0016987 IPR012760
GO:0006352 IPR012760
GO:0006355 IPR012760

4 Ontology Annotations

GO Term Gene Name
GO:0003677 IPR012760
GO:0016987 IPR012760
GO:0006352 IPR012760
GO:0006355 IPR012760

1 Parent Features

DB identifier Type Name
IPR000943 Domain RNA polymerase sigma-70

4 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
Araha.11756s0302.1.p PAC:28856318 Arabidopsis halleri 613  
Brdisv1pangenome1000625m.p PAC:33659139 Brachypodium distachyon Pangenome 249  
Brdisv1BdTR11G1006483m.p PAC:34605350 Brachypodium distachyon BdTR11g 249  
Brdisv1BdTR11A1041581m.p PAC:35689232 Brachypodium distachyon BdTR11a 544  

5 Publications

First Author Title Year Journal Volume Pages PubMed ID
            3052291
            1597408
            3092189
            11931761
            8858155