Editing Sigma factor (section)

== Structure ==
[[File:Sigma 70 domains.png|thumb|right|Domain organization, promoter recognition and structural organization of the σ<sup>70</sup> family. ('''a''') The domain organization of σ factors from Groups 1, 3 and 4 are illustrated above σ<sup>70</sup> consensus E. coli promoter DNA. ('''b''') Organization of E. coli σ70 in an RNA polymerase transcription initiation complex. (PDB 4YLN).]]

By sequence similarity, most sigma factors are σ<sup>70</sup>-like ({{InterPro|IPR000943}}). They have four main regions (domains) that are generally conserved:

 N-terminus --------------------- C-terminus
              1.1    2    3    4

The regions are further subdivided. For example, region 2 includes 1.2 and 2.1 through 2.4.

Domain 1.1 is found only in "primary sigma factors" (RpoD, RpoS in ''E.coli''; "Group 1").  It is involved in ensuring the sigma factor will only bind the promoter when it is complexed with the RNA polymerase.<ref name="pmid26131973">{{cite journal | vauthors = Paget MS | title = Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution | journal = Biomolecules | volume = 5 | issue = 3 | pages = 1245–65 | date = June 2015 | pmid = 26131973 | pmc = 4598750 | doi = 10.3390/biom5031245 | doi-access = free }}</ref> Domains 2-4 each interact with specific promoter elements and with RNAP. Region 2.4 recognizes and binds to the promoter −10 element (called the "[[Pribnow box]]"). Region 4.2 recognizes and binds to the promoter −35 element.<ref name="pmid26131973"/>

Not every sigma factor of the σ<sup>70</sup> family contains all the domains. Group 2, which includes RpoS, is very similar to Group 1 but lacks domain 1. Group 3 also lacks domain 1, and includes σ<sup>28</sup>. Group 4, also known as the Extracytoplasmic Function (ECF) group, lack both σ1.1 and σ3. RpoE is a member.<ref name="pmid26131973"/>

{{further|RpoN}}
Other known sigma factors are of the σ<sup>54</sup>/RpoN ({{InterPro|IPR000394}}) type. They are functional sigma factors, but they have significantly different primary amino acid sequences.<ref>{{cite journal | vauthors = Merrick MJ | title = In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N) | journal = Molecular Microbiology | volume = 10 | issue = 5 | pages = 903–9 | date = December 1993 | pmid = 7934866 | doi = 10.1111/j.1365-2958.1993.tb00961.x | s2cid = 84789281 }}</ref>

<div style="max-width: 100%; overflow-x: scroll; clear: both">
{|class="wikitable mw-collapsible"
|+Protein domain infoboxes
|-
|{{Infobox protein family
| Symbol = Sigma70_r1_1
| Name = Sigma70 region 1.1
| image = 
| width = 
| caption = Autoregulation of a group 1 bacterial sigma factor involves the formation of a region 1.1- induced compacted structure
| Pfam = PF03979
| Pfam_clan =  
| InterPro = IPR007127
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
|{{Infobox protein family
| Symbol = Sigma70_r1_2
| Name = Sigma70 region 1.2
| image = PDB 1ku2 EBI.jpg
| width = 
| caption = Crystal structure of ''Thermus aquaticus'' RNA polymerase sigma subunit fragment containing regions 1.2 to 3.1
| Pfam = PF00140
| Pfam_clan =  
| InterPro = IPR009042
| SMART = 
| PROSITE = PDOC00592
| MEROPS = 
| SCOP = 1sig
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
|{{Infobox protein family
| Symbol = Sigma70_r2
| Name = Sigma70 region 2
| image = PDB 1sig EBI.jpg
| width = 
| caption = Crystal structure of a sigma70 subunit fragment from ''Escherichia coli'' RNA polymerase
| Pfam = PF04542
| Pfam_clan = CL0123
| InterPro = IPR007627
| SMART = 
| PROSITE = PDOC00592
| MEROPS = 
| SCOP = 1sig
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
|{{Infobox protein family
| Symbol = Sigma70_r3
| Name = Sigma70 region 3
| image = PDB 1rp3 EBI.jpg
| width = 
| caption = Solution structure of sigma70 region 3 from ''Thermotoga maritima''
| Pfam = PF04539
| Pfam_clan = CL0123
| InterPro = IPR007624
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 1ku2
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
|{{Infobox protein family
| Symbol = Sigma70_r4
| Name = Sigma70 region 4
| image = PDB 1tty EBI.jpg
| width = 
| caption = Solution structure of sigma70 region 4 from ''Thermotoga maritima''
| Pfam = PF04545
| Pfam_clan = CL0123
| InterPro = IPR007630
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 1or7
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
|{{Infobox protein family
| Symbol = Sigma70_r4_2
| Name = Sigma70 region 4.2
| image = PDB 2h27 EBI.jpg
| width = 
| caption = Crystal structure of ''Escherichia coli'' sigma70 region 4 bound to its -35 element DNA
| Pfam = PF08281
| Pfam_clan = CL0123
| InterPro = IPR013249
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 1or7
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
|}
</div>