Conserved Site

Transcription regulator HTH, Crp-type, conserved site (IPR018335)

Short name: Tscrpt_reg_HTH_Crp-type_CS


The crp-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 70-75 amino acids present in transcription regulators of the crp-fnr family, involved in the control of virulence factors, enzymes of aromatic ring degradation, nitrogen fixation, photosynthesis, and various types of respiration. The crp-fnr family is named after the first members identified in Escherichia coli: the well characterised cyclic AMP receptor protein CRP or CAP (catabolite activator protein) and the fumarate and nitrate reductase regulator Fnr. crp-type HTH domain proteins occur in most bacteria and in chloroplasts of red algae. The DNA-binding HTH domain is located in the C-terminal part; the N-terminal part of the proteins of the crp-fnr family contains a nucleotide-binding domain and a dimerisation/linker helix occurs in between. The crp-fnr regulators predominantly act as transcription activators, but can also be important repressors, and respond to diverse intracellular and exogenous signals, such as cAMP, anoxia, redox state, oxidative and nitrosative stress, carbon monoxide, nitric oxide or temperature [PMID: 8441692].

The structure of the crp-type DNA-binding domain shows that the helices (H) forming the helix-turn-helix motif (H2-H3) are flanked by two beta-hairpin (B) wings, in the topology H1-B1-B2-H2-H3-B3-B4. Helix 3 is termed the recognition helix, as in most wHTHs it binds the DNA major groove [PMID: 10550204, PMID: 11017196, PMID: 11839496].

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

  • E. coli crp (also known as cAMP receptor), a protein that complexes with cAMP and regulates the transcription of several catabolite-sensitive operons.
  • E. coli fnr, a protein that activates genes for proteins involved in a variety of anaerobic electron transport systems.
  • Rhizobium leguminosarum fnrN, a transcription regulator of nitrogen fixation.
  • Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides) fnrL, a transcription activator of genes for heme biosynthesis, bacteriochlorophyll synthesis and the light-harvesting complex LHII.
  • Rhizobiacae fixK, a protein that regulates nitrogen fixation genes, both positively and negatively.
  • Lactobacillus casei fnr-like protein flp, a putative regulatory protein linked to the trpDCFBA operon.
  • Cyanobacteria ntcA, a regulator of the expression of genes subject to nitrogen control.
  • Xanthomonas campestris clp, a protein involved in the regulation of phytopathogenicity. Clp controls the production of extracellular enzymes, xanthan gum and pigment, either positively or negatively.

GO terms

Biological Process

GO:0006355 regulation of transcription, DNA-templated

Molecular Function

GO:0003700 DNA binding transcription factor activity

Cellular Component

GO:0005622 intracellular

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE patterns