InterPro : IPR000551

Name  MerR-type HTH domain Short Name  MerR-type_HTH_dom
Type  Domain Description  The merR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH)domain of about 70 residues present in the merR family of transcriptionalregulators []. MerR-type regulators are present in diverse bacterial genera, in the cytoplasm. The helix-turn-helix DNA-binding motif is located in the N-terminal part of these transcriptional regulators and is followed by a coiled-coil region. The C-terminal part of merR-type regulators contains effector binding regions that are specific to the effector recognised. Most merR-type transcriptional regulators respond to environmental stimuli, like heavy metals, oxidative stress or antibiotics and a subgroup of metalloregulators are bacterial transcription activators that respond to metal ions [].Several structures of merR-type transcriptional regulators have been resolvedand their N-terminal DNA-binding domains are ascribed to the superfamily ofwinged-helix proteins, containing a four-helix (H) bundle and a three-strandedantiparallel beta-sheet (B) in the topology: B1-H1-H2-B2-B3-H3-H4 []. The helix-turn-helix motif comprises the first and secondhelices, the second being called the recognition helix. The HTH is involved inDNA-binding into the major groove, where the recognition helix makes mostDNA-contacts. The second DNA-binding element is wing W1, composed of thesecond and third beta-strands and their connecting loop. The third DNA-bindingelement, wing W2, is not a loop like in typical winged-helix proteins, butanother H-T-H motif formed by helices three and four. In a typical merRregulator, the HTH and two wings bind the promoter of the regulated operonbetween the -35 and -10 regions in a spacer of 19/20 bp and longer than usual,distorting the operator DNA and causing RNA polymerase to initiatetranscription []. Most merR-like transcriptional regulators are dimers.Some proteins known to contain a merR-type HTH domain:Tn501 merR, mercuric resistance operon regulatory protein. In the absenceof mercury merR represses transcription by binding tightly, as a dimer, tothe 'mer' operator region; when mercury is present the dimeric complexbinds a single ion and becomes a potent transcriptional activator, whileremaining bound to the mer site.Bacillus subtilis bltR, bmrR and mtaN (ywnD), transcriptional activators ofthe blr and bmr transporters involved in multidrug resistance.Escherichia coli soxR, responds to oxidative stress and autoregulatory controls a superoxide response regulon.Bradyrhizobium japonicum nolA, a transcriptional regulator involved in the genotype-specific nodulation of soybeans.Streptomyces lividans tipA, a transcriptional activator which binds to and is activated by the antibiotic thiostrepton.Escherichia coli zntR, a zinc-responsive regulator of zntA ATPase.Escherichia coli cueR , a regulator of the copper efflux regulon.CarA (Q1DDV9) and CarH (Q1DDV8) from Myxococcus xanthus, paralogous repressors that requires B(12) to down-regulation of a light-inducible promoter [, ]. TtCarH (Q746J7) from Thermus thermophilus, belongs to a class of photoreceptors that use 5'-deoxyadenosylcobalamin (AdoB12) as the light-sensing chromophore [].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



0 Child Features

0 Contains

8 Found In

Id Name Short Name Type
IPR017818 Plasmid partitioning protein, RepA Plasmid_partition_RepA Family
IPR010093 SinI-like, DNA-binding domain SinI_DNA-bd Domain
IPR010211 Redox-sensitive transcriptional activator SoxR Redox-sen_tscrpt-act_SoxR Family
IPR011788 Zn(II)-responsive transcriptional regulator ZntR Family
IPR011789 Cu(I)-responsive transcriptional regulator CueR Family
IPR011791 Cd(II)/Pb(II)-responsive transcriptional regulator CadR-PbrR Family
IPR011794 Hg(II)-responsive transcriptional regulator MerR Family
IPR011797 Mercuric resistence transcriptional repressor protein MerD MerD Family

1 Parent Features

Id Name Short Name Type
IPR009061 DNA binding domain, putative DNA-bd_dom_put Domain

6 Publications

First Author Title Year Journal Volume Pages
Helmann JD Homologous metalloregulatory proteins from both gram-positive and gram-negative bacteria control transcription of mercury resistance operons. 1989 J Bacteriol 171 222-9
Brown NL The MerR family of transcriptional regulators. 2003 FEMS Microbiol Rev 27 145-63
Godsey MH Structural biology of bacterial multidrug resistance gene regulators. 2002 J Biol Chem 277 40169-72
Ortiz-Guerrero JM Light-dependent gene regulation by a coenzyme B12-based photoreceptor. 2011 Proc Natl Acad Sci U S A 108 7565-70
Díez AI Analytical ultracentrifugation studies of oligomerization and DNA-binding of TtCarH, a Thermus thermophilus coenzyme B12-based photosensory regulator. 2013 Eur Biophys J 42 463-76
Pérez-Marín MC Vitamin B12 partners the CarH repressor to downregulate a photoinducible promoter in Myxococcus xanthus. 2008 Mol Microbiol 67 804-19

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)