Protein Domain : IPR013324

Type:  Domain Name:  RNA polymerase sigma factor, region 3/4
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. Short Name:  RNA_pol_sigma_r3_r4
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1 Child Features

DB identifier Type Name
IPR013249 Domain RNA polymerase sigma factor 70, region 4 type 2

2 Contains

DB identifier Type Name
IPR007630 Domain RNA polymerase sigma-70 region 4
IPR007624 Domain RNA polymerase sigma-70 region 3

1 Cross References

Identifier
SSF88659

20 Found Ins

DB identifier Type Name
IPR011991 Domain Winged helix-turn-helix DNA-binding domain
IPR014284 Domain RNA polymerase sigma-70 like domain
IPR000943 Domain RNA polymerase sigma-70
IPR016262 Family RNA polymerase sigma factor, SigB/C/D/F, plastid
IPR012759 Family RNA polymerase sigma factor RpoH, proteobacteria
IPR012760 Domain RNA polymerase sigma factor RpoD, C-terminal
IPR017848 Family RNA polymerase sigma factor, RpoD-like, cyanobacteria
IPR014209 Family RNA polymerase sigma-K type
IPR012761 Family RNA polymerase sigma factor RpoS
IPR014200 Family RNA polymerase sigma-E type
IPR012845 Family RNA polymerase sigma factor, FliA/WhiG
IPR014305 Family RNA polymerase sigma-G type, actinobacteria
IPR014322 Family RNA polymerase sigma-B/F/G type
IPR014236 Family RNA polymerase sigma-F type
IPR014288 Family RNA polymerase sigma-B factor
IPR014212 Family RNA polymerase sigma-G type
IPR014300 Family RNA polymerase sigma-V type
IPR011517 Family RNA polymerase sigma-70 ECF-like
IPR014294 Family RNA polymerase sigma-W, bacillaceae
IPR007394 Family Putative helix-turn-helix protein, YlxM/p13-like

5 GO Annotations

GO Term Gene Name
GO:0003677 IPR013324
GO:0003700 IPR013324
GO:0016987 IPR013324
GO:0006352 IPR013324
GO:0006355 IPR013324

5 Ontology Annotations

GO Term Gene Name
GO:0003677 IPR013324
GO:0003700 IPR013324
GO:0016987 IPR013324
GO:0006352 IPR013324
GO:0006355 IPR013324

0 Parent Features

3256 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
147096 D8RGX1 PAC:15401952 Selaginella moellendorffii 458  
53596 D8S3G8 PAC:15415781 Selaginella moellendorffii 326  
117159 D8SHL6 PAC:15403291 Selaginella moellendorffii 292  
266972 D8R5F3 PAC:15412233 Selaginella moellendorffii 249  
evm.model.supercontig_125.39 PAC:16407269 Carica papaya 443  
evm.model.supercontig_20.169 PAC:16412969 Carica papaya 276  
evm.model.supercontig_3.54 PAC:16416838 Carica papaya 547  
evm.model.supercontig_3807.1 PAC:16418945 Carica papaya 333  
evm.model.supercontig_43.154 PAC:16419967 Carica papaya 301  
evm.model.supercontig_56.16 PAC:16422721 Carica papaya 564  
evm.model.supercontig_73.29 PAC:16425606 Carica papaya 357  
29794.m003368 B9RRX0 PAC:16808728 Ricinus communis 560  
29864.m001444 B9RVK0 PAC:16811756 Ricinus communis 389  
30078.m002307 B9S0J0 PAC:16817418 Ricinus communis 548  
30148.m001412 B9SDA3 PAC:16820557 Ricinus communis 569  
30148.m001468 B9SDF8 PAC:16820612 Ricinus communis 508  
30169.m006532 B9RIL8 PAC:16821332 Ricinus communis 501  
30892.m000027 B9TKG6 PAC:16824679 Ricinus communis 190  
32775.m000024 B9TEC6 PAC:16825552 Ricinus communis 271  
33001.m000032 PAC:16825645 Ricinus communis 122  
33296.m000030 B9TG49 PAC:16825763 Ricinus communis 124  
34613.m000038 B9TJU4 PAC:16826284 Ricinus communis 139  
34894.m000025 B9TKF6 PAC:16826395 Ricinus communis 90  
36669.m000026 B9TNB3 PAC:16826954 Ricinus communis 75  
44451.m000025 B9TIA7 PAC:16827700 Ricinus communis 68  
28920.m000046 PAC:16801985 Ricinus communis 169  
Cucsa.362600.1 A0A0A0K917 PAC:16980950 Cucumis sativus 580  
Cucsa.012950.1 PAC:16951584 Cucumis sativus 585  
Cucsa.012950.2 A0A0A0LCQ9 PAC:16951585 Cucumis sativus 547  
Cucsa.124610.1 A0A0A0KEQ6 PAC:16961743 Cucumis sativus 562  

6 Publications

First Author Title Year Journal Volume Pages PubMed ID
            3052291
            1597408
            3092189
            11931761
            8858155
            11955433