PROSITE documentation PDOC00043

LysR-type HTH domain profile

The lysR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 60 residues present in lysR-type transcriptional regulators (LTTR), one of the most common regulator families in prokaryotes. The family is named after the Escherichia coli regulator lysR [1]. LysR proteins are present in diverse bacterial genera, archaea and algal chloroplasts. All LTTRs contain the DNA-binding lysR-type HTH domain, usually in the N-terminal part. Most LTTRs require a small compound that acts as co-inducer. The C-terminal part of lysR proteins can contain a regulatory domain with two subdomains involved in (1) co-inducer recognition/response and (2) DNA binding and response. LTTRs activate the transcription of operons and regulons involved in very diverse functions, such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, regulation of virulence factors, nodulation for nitrogen fixing bacteria, oxidative stress response or aromatic compounds catabolism.

Most LTTRs act as a transcriptional activator of the target genes and also as a repressor of their own expression. Typical LTTRs bind to a sequence of about 50-60 bp, which contains two distinct sites, (1) a recognition-binding site (RBS) centered near -65 of the target transcription start site and with an inverted repeat motif including the T-N(11)-A motif and (2) an activation-binding site (ABS) which overlaps the -35 region of the transcription start site of the regulated gene. LysR proteins are mainly cytoplasmic, but some seem membrane-bound [2].

The crystal structure of the lysR DNA-binding domain of CbnR shows three α helices and two anti-parallel β strands (see <PDB:1IXC>), with the helix-turn-helix motif comprising the second and third helices and the strands being called the wing. Most LTTRs are likely tetramers [3].

Some proteins known to contain a lysR domain:

• Proteus vulgaris blaA, a transcriptional regulator of β-lactamase.
• Pseudomonas putida catR, a regulator of catechol catabolism for benzoate degradation.
• Escherichia coli cynR, a regulator for detoxification of cyanate.
• Klebsiella aerogenes cysB, a regulator of cysteine biosynthesis.
• Vibrio cholerae irgB, an iron-dependent regulator of virulence factors.
• Escherichia coli lysR, a transcriptional regulator of lysine biosynthesis.
• Escherichia coli nhaR, a regulator of a sodium/proton (Na+/H+) antiporter.
• Rhizobium meliloti nodD and syrM, regulators of nodulation genes involved in nitrogen fixation symbiosis.
• Salmonella typhimurium oxyR, a regulator of intracellular hydrogen peroxide and oxydative stress response.
• Ralstonia solanacearum phcA, a regulator of virulence factors.

The profile we developed covers the entire lysR-type HTH domain.