RNA polymerase sigma factor 54 (IPR000394)

Short name: RNA_pol_sigma_54

Overlapping homologous superfamilies


Family relationships



Sigma factors [PMID: 3052291] are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943). The sigma-54 family consists exclusively of sigma-54 factor [PMID: 2517036, PMID: 7934866] required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognised by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions:

  1. A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif.
  2. A region of variable length which is not well conserved.
  3. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known.

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0001216 bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding
GO:0016987 sigma factor activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE patterns
PROSITE patterns