{PDOC00562}
{PS00654; PRD_1}
{PS51372; PRD_2}
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* PRD domain profile and signature *
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Transcriptional antiterminators and activators containing phosphoenolpyruvate:
sugar phosphotransferase  system  (PTS) regulation domains (PRDs) form a class
of bacterial    regulatory   proteins   whose   activity   is   modulated   by
phosphorylation. These  regulators  stimulate  the  expression  of  genes  and
operons involved  in  carbohydrate  metabolism. They are  characterized by the
presence of  a  duplicated  regulatory  module  of  ~100  residues that can be
reversibly phosphorylated   on   histidyl   residues   by  the  PTS.  PRDs  in
transcriptional antiterminators and activators are PTS regulatory targets that
are (de)phosphorylated  in  response  to  the  availability  of carbon sources
[1-5].

The PRD  domain  comprises  one  and often two highly conserved histidines. It
forms a   compact   bundle   comprising   five  helices  (alpha1-alpha5)  (see
<PDB:1H99>). The  core of the PRD module consists of two pairs of antiparallel
helices making  an  angle  of  ~60°. The first pairs contains the antiparallel
helices alpha1  and  alpha4, while the second pair contains alpha2 and alpha5.
The third  helix  (alpha3)  is  oriented  perpendicularly  to  alpha5  at  the
periphery of  the bundle. The helices are connected by loops of varying length
[3-5].

Some proteins known to contain a PRD domain are listed below:

 - Escherichia  coli bglG, which mediates the positive regulation of the beta-
   glucoside (bgl) operon by functioning as a transcriptional antiterminator.
 - Bacillus  subtilis licT, which regulates the expression of operons involved
   in beta-glucoside metabolism.
 - Bacillus subtilis licR, the probable licABCH operon regulator.
 - Bacillus  subtilis  levR,  which  regulates  the expression of the levanase
   operon (levDEFG and sacC). LevR is  composed  of  two domains: a N-terminal
   section that contains a  sigma-54 factor interaction ATP-binding domain and
   a C-terminal  bglG-like  domain.  LevR  could  be phosphorylated by levD or
   levE.
 - Bacillus  subtilis  sacT,  which  regulates  the  expression of the sucrose
   operon (sacPA). SacT is probably phosphorylated by sacP (EII-scr).
 - Bacillus  subtilis sacY, which regulates the expression of the levansucrase
   operon (sacBX). SacY is probably phosphorylated by the sacX protein.
 - Bacillus stearothermophilus mtlR activator.
 - Erwinia  chrysanthemi  arbG  [6],  which is involved in the regulation of a
   beta-glucoside operon. ArbG is probably phosphorylated by arbF (EII-bgl).
 - Lactobacillus casei lacT [7], involved in the regulation of the lac operon.

As a signature pattern for the PRD domain, we selected a conserved region that
includes a  conserved  histidine that could be the site of phosphorylation. We
have also developed a profile, which covers the entire PRD domain.

-Consensus pattern: [ST]-[DM]-H-[LIC]-x(2)-[FA]-[LIY]-[EQK]-R-x(2)-[QNKA]
                    [H could be phosphorylated]
-Sequences known to belong to this class detected by the pattern: ALL.
-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: March 2008 / Text revised; profile added.

[ 1] Tortosa P., Aymerich S., Lindner C., Saier M.H. Jr., Reizer J.,
     Le Coq D.
     "Multiple phosphorylation of SacY, a Bacillus subtilis transcriptional
     antiterminator negatively controlled by the phosphotransferase
     system."
     J. Biol. Chem. 272:17230-17237(1997).
     PubMed=9202047
[ 2] Stuelke J., Arnaud M., Rapoport G., Martin-Verstraete I.
     "PRD--a protein domain involved in PTS-dependent induction and carbon
     catabolite repression of catabolic operons in bacteria."
     Mol. Microbiol. 28:865-874(1998).
     PubMed=9663674
[ 3] van Tilbeurgh H., Declerck N.
     "Structural insights into the regulation of bacterial signalling
     proteins containing PRDs."
     Curr. Opin. Struct. Biol. 11:685-693(2001).
     PubMed=11751049
[ 4] van Tilbeurgh H., Le Coq D., Declerck N.
     "Crystal structure of an activated form of the PTS regulation domain
     from the LicT transcriptional antiterminator."
     EMBO J. 20:3789-3799(2001).
     PubMed=11447120; DOI=10.1093/emboj/20.14.3789
[ 5] Graille M., Zhou C.-Z., Receveur-Brechot V., Collinet B., Declerck N.,
     van Tilbeurgh H.
     "Activation of the LicT transcriptional antiterminator involves a
     domain swing/lock mechanism provoking massive structural changes."
     J. Biol. Chem. 280:14780-14789(2005).
     PubMed=15699035; DOI=10.1074/jbc.M414642200
[ 6] El Hassouni M., Henrissat B., Chippaux M., Barras F.
     "Nucleotide sequences of the arb genes, which control beta-glucoside
     utilization in Erwinia chrysanthemi: comparison with the Escherichia
     coli bgl operon and evidence for a new beta-glycohydrolase family
     including enzymes from eubacteria, archaebacteria, and humans."
     J. Bacteriol. 174:765-777(1992).
     PubMed=1732212
[ 7] Alpert C.-A., Siebers U.
     "The lac operon of Lactobacillus casei contains lacT, a gene coding
     for a protein of the Bg1G family of transcriptional antiterminators."
     J. Bacteriol. 179:1555-1562(1997).
     PubMed=9045813

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