PROSITE documentation PDOC00696

DeoR-type HTH domain signature and profile





Description

The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after Escherichia coli deoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively.

DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerization domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [1,2,3].

Some proteins known to contain a deoR-type HTH domain:

  • Escherichia coli deoR, a transcription repressor of the operon for deoxyribose metabolism. The effector is deoxyribose-5-phosphate.
  • Escherichia coli glpR, a glycerol-3-phosphate regulon repressor.
  • Lactococcus lactis lacR, a lactose phosphotransferase system repressor.
  • Agrobacterium tumefaciens plasmid pTiC58 accR, a transcription repressor of agrocinopine catabolism and conjugal transfer.
  • Escherichia coli agaR, a repressor of the aga operon for metabolism of N-acetylgalactosamine and galactosamine [3].
  • Escherichia coli fucR, an activator of operons for L-fucose utilization.
  • Escherichia coli gatR, a repressor of the galactitol operon.
  • Escherichia coli srlR (gutR), a glucitol operon repressor.
  • Bacillus subtilis iolR, a repressor of inositol operons.

The pattern we use to detect these proteins starts fourteen residues before the HTH motif and ends one residue after it. The profile we developed extends seventeen residues upstream and seventeen residues downstream of the HTH extremities and covers the entire deoR-type HTH DNA-binding domain.

Note:

The deoR repressor from Bacillus subtilis, which regulates expression of the dra-nupC-pdp operon required for deoxyribonucleoside and deoxyribose utilization, shows no sequence similarity to E. coli deoR. There is no similarity in the DNA operator sites either and the B. subtilis deoR does not possess a deoR-type HTH domain.

Last update:

December 2004 / Pattern and text revised.

Technical section

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

HTH_DEOR_2, PS51000; DeoR-type HTH domain profile  (MATRIX)

HTH_DEOR_1, PS00894; DeoR-type HTH domain signature  (PATTERN)


References

1AuthorsBeck von Bodman S., Hayman G.T., Farrand S.K.
TitleOpine catabolism and conjugal transfer of the nopaline Ti plasmid pTiC58 are coordinately regulated by a single repressor.
SourceProc. Natl. Acad. Sci. U.S.A. 89:643-647(1992).
PubMed ID1731335

2AuthorsBairoch A.
SourceUnpublished observations (1993).

3AuthorsRay W.K., Larson T.J.
TitleApplication of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12.
SourceMol. Microbiol. 51:813-826(2004).
PubMed ID14731281



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