{PDOC00579}
{PS00675; SIGMA54_INTERACT_1}
{PS00676; SIGMA54_INTERACT_2}
{PS00688; SIGMA54_INTERACT_3}
{PS50045; SIGMA54_INTERACT_4}
{BEGIN}
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* 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.

-Consensus pattern: [LIVMFY](3)-x-G-[DEQ]-[STE]-G-[STAV]-G-K-x(2)-[LIVMFY]
-Sequences known to belong to this class detected by the pattern: A majority.
-Other sequence(s) detected in Swiss-Prot: eukaryotic rab-like ypt1  family of
 GTP-binding proteins.

-Consensus pattern: [GS]-x-[LIVMFA]-x(2)-[AS]-[DNEQASH]-[GNEKT]-G-[STIM]-
                    [LIVMFY](3)-[DE]-[EK]-[LIVM]
-Sequences known to belong to this class detected by the pattern: A majority.
-Other sequence(s) detected in Swiss-Prot: 1.

-Consensus pattern: [FYW]-P-[GS]-N-[LIVM]-R-[EQ]-L-x-[NHAT]
-Sequences known to belong to this class detected by the pattern: Almost   all
 of these proteins.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: April 2006 / Pattern revised.

[ 1] Morrett E., Segovia L.
     J. Bacteriol. 175:6067-6074(1993).
[ 2] Austin S., Kundrot C., Dixon R.
     "Influence of a mutation in the putative nucleotide binding site of
     the nitrogen regulatory protein NTRC on its positive control
     function."
     Nucleic Acids Res. 19:2281-2287(1991).
     PubMed=2041769
[ 3] Albright L.M., Huala E., Ausubel F.M.
     "Prokaryotic signal transduction mediated by sensor and regulator
     protein pairs."
     Annu. Rev. Genet. 23:311-336(1989).
     PubMed=2694934; DOI=10.1146/annurev.ge.23.120189.001523
[ 4] Austin S., Dixon R.
     "The prokaryotic enhancer binding protein NTRC has an ATPase activity
     which is phosphorylation and DNA dependent."
     EMBO J. 11:2219-2228(1992).
     PubMed=1534752

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