PROSITE documentation PDOC00579
Sigma-54 interaction domain signatures and profile


Some bacterial regulatory proteins activate the expression of genes from promoters recognized by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [1,2] interaction with sigma-54. This domain has been found in the proteins listed below:

  • acoR from Alcaligenes eutrophus, an activator of the acetoin catabolism operon acoXABC.
  • algB from Pseudomonas aeruginosa, an activator of alginate biosynthetic gene algD.
  • dctD from Rhizobium, an activator of dctA, the C4-dicarboxylate transport protein.
  • dhaR from Citrobacter freundii, a regulator of the dha operon for glycerol utilization.
  • fhlA from Escherichia coli, an activator of the formate dehydrogenase H and hydrogenase III structural genes.
  • flbD from Caulobacter crescentus, an activator of flagellar genes.
  • hoxA from Alcaligenes eutrophus, an activator of the hydrogenase operon.
  • hrpS from Pseudomonas syringae, an activator of hprD as well as other hrp loci involved in plant pathogenicity.
  • hupR1 from Rhodobacter capsulatus, an activator of the [NiFe] hydrogenase genes hupSL.
  • hydG from Escherichia coli and Salmonella typhimurium, an activator of the hydrogenase activity.
  • levR from Bacillus subtilis, which regulates the expression of the levanase operon (levDEFG and sacC).
  • nifA (as well as anfA and vnfA) from various bacteria, an activator of the nif nitrogen-fixing operon.
  • ntrC, from various bacteria, an activator of nitrogen assimilatory genes such as that for glutamine synthetase (glnA) or of the nif operon.
  • pgtA from Salmonella typhimurium, the activator of the inducible phospho- glycerate transport system.
  • pilR from Pseudomonas aeruginosa, an activator of pilin gene transcription.
  • rocR from Bacillus subtilis, an activator of genes for arginine utilization
  • tyrR from Escherichia coli, involved in the transcriptional regulation of aromatic amino-acid biosynthesis and transport.
  • wtsA, from Erwinia stewartii, an activator of plant pathogenicity gene wtsB.
  • xylR from Pseudomonas putida, the activator of the tol plasmid xylene catabolism operon xylCAB and of xylS.
  • Escherichia coli hypothetical protein yfhA.
  • Escherichia coli hypothetical protein yhgB.

About half of these proteins (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [3] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section.

The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction [4]. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain; we have developed signature patterns for both motifs. Other regions of the domain are also conserved. We have selected one of them, located in the C-terminal section, as a third signature pattern.

Last update:

April 2006 / Pattern revised.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

SIGMA54_INTERACT_4, PS50045; Sigma-54 interaction domain profile  (MATRIX)

SIGMA54_INTERACT_1, PS00675; Sigma-54 interaction domain ATP-binding region A signature  (PATTERN)

SIGMA54_INTERACT_2, PS00676; Sigma-54 interaction domain ATP-binding region B signature  (PATTERN)

SIGMA54_INTERACT_3, PS00688; Sigma-54 interaction domain C-terminal part signature  (PATTERN)


1AuthorsMorrett E. Segovia L.
SourceJ. Bacteriol. 175:6067-6074(1993).

2AuthorsAustin S. Kundrot C. Dixon R.
TitleInfluence of a mutation in the putative nucleotide binding site of the nitrogen regulatory protein NTRC on its positive control function.
SourceNucleic Acids Res. 19:2281-2287(1991).
PubMed ID2041769

3AuthorsAlbright L.M. Huala E. Ausubel F.M.
TitleProkaryotic signal transduction mediated by sensor and regulator protein pairs.
SourceAnnu. Rev. Genet. 23:311-336(1989).
PubMed ID2694934

4AuthorsAustin S. Dixon R.
TitleThe prokaryotic enhancer binding protein NTRC has an ATPase activity which is phosphorylation and DNA dependent.
SourceEMBO J. 11:2219-2228(1992).
PubMed ID1534752

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