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
algB from Pseudomonas aeruginosa, an activator of alginate biosynthetic
dctD from Rhizobium, an activator of dctA, the C4-dicarboxylate transport
dhaR from Citrobacter freundii, a regulator of the dha operon for glycerol
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
hydG from Escherichia coli and Salmonella typhimurium, an activator of the
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
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
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  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 . 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.
PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and
distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives
(CC BY-NC-ND 4.0) License, see prosite_license.html.