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PROSITE documentation PDOC00562 [for PROSITE entry PS00654]

PRD domain profile and signature





Description

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 [1,2,3,4,5].

The PRD domain comprises one and often two highly conserved histidines. It forms a compact bundle comprising five helices (α1-α5) (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 α1 and α4, while the second pair contains α2 and α5. The third helix (α3) is oriented perpendicularly to α5 at the periphery of the bundle. The helices are connected by loops of varying length [3,4,5].

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

  • Escherichia coli bglG, which mediates the positive regulation of the β- glucoside (bgl) operon by functioning as a transcriptional antiterminator.
  • Bacillus subtilis licT, which regulates the expression of operons involved in β-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 β-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.

Last update:

March 2008 / Text revised; profile added.

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Technical section

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

PRD_1, PS00654; PRD domain signature  (PATTERN)

PRD_2, PS51372; PRD domain profile  (MATRIX)


References

1AuthorsTortosa P. Aymerich S. Lindner C. Saier M.H. Jr. Reizer J. Le Coq D.
TitleMultiple phosphorylation of SacY, a Bacillus subtilis transcriptional antiterminator negatively controlled by the phosphotransferase system.
SourceJ. Biol. Chem. 272:17230-17237(1997).
PubMed ID9202047

2AuthorsStuelke J. Arnaud M. Rapoport G. Martin-Verstraete I.
TitlePRD--a protein domain involved in PTS-dependent induction and carbon catabolite repression of catabolic operons in bacteria.
SourceMol. Microbiol. 28:865-874(1998).
PubMed ID9663674

3Authorsvan Tilbeurgh H. Declerck N.
TitleStructural insights into the regulation of bacterial signalling proteins containing PRDs.
SourceCurr. Opin. Struct. Biol. 11:685-693(2001).
PubMed ID11751049

4Authorsvan Tilbeurgh H. Le Coq D. Declerck N.
TitleCrystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator.
SourceEMBO J. 20:3789-3799(2001).
PubMed ID11447120
DOI10.1093/emboj/20.14.3789

5AuthorsGraille M. Zhou C.-Z. Receveur-Brechot V. Collinet B. Declerck N. van Tilbeurgh H.
TitleActivation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes.
SourceJ. Biol. Chem. 280:14780-14789(2005).
PubMed ID15699035
DOI10.1074/jbc.M414642200

6AuthorsEl Hassouni M. Henrissat B. Chippaux M. Barras F.
TitleNucleotide 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.
SourceJ. Bacteriol. 174:765-777(1992).
PubMed ID1732212

7AuthorsAlpert C.-A. Siebers U.
TitleThe lac operon of Lactobacillus casei contains lacT, a gene coding for a protein of the Bg1G family of transcriptional antiterminators.
SourceJ. Bacteriol. 179:1555-1562(1997).
PubMed ID9045813



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