PROSITE documentation PDOC00661

ArsR-type HTH domain signature and profile

The arsR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 90-100 amino acids present in transcription regulators of the arsR/smtB family, involved in stress-response to heavy metal ions. This family of prokaryotic metal-sensing transcription repressors is named after Escherichia coli arsR, an arsenic-responsive repressor of the ars operon for arsenate reductase and metal ion extrusion, and after Synechococcus PCC 7942 smtB, a Zn(II)-responsive repressor of the smtA gene for a Zn sequestering metallothionein [1]. ArsR/smtB-like repressors of metal resistance operons specifically bind to the operator/promoter and seem to dissociate from the DNA in the presence of metal ions, permitting transcription of proteins involved in metal-ions efflux and/or detoxification. The arsR/smtB family includes transcription repressors responsive to Zn(II), As(III), Cd(II), Pb(II), Bi(III), Co(II), Ni(II), Cu(I), and Ag(I) [1,2].

The crystal structure of the cyanobacterial smtB shows a fold of five α-helices (H) and a pair of antiparallel β-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5 (see <PDB:1SMT>). Helices 3 and 4 comprise the helix-turn-helix motif and the β-sheet is called the wing as in other wHTH, such as the dtxR-type (see <PDOC50944>) or the merR-type (see <PDOC00477>). Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers [3]. The dimer interface is formed by helix 5 and an N-terminal part [4]. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N-terminus, called the α3(N) site [5,1,3]. The second metal-binding site is located in helix 5 (and C-terminus) and is called the α5(C) site. The α3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its α3 site coordinates smaller thiophilic ions like As and Sb. The α5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [1,2]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promoter DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognized by multimeric arsR-type metalloregulators.

Some proteins known to contain an arsR-type HTH domain:

• Escherichia coli arsR, an arsenic-responsive transcription repressor of the arsenic resistance operon (ars) which encodes an arsenate reductase and metal exporters.
• Synechococcus PCC 7942 smtB, a Zn(II)-responsive transcription repressor of the smtA gene that codes for a metallothionein. SmtB senses Co(II) and Cd(II) too, but Zn(II) is the preferred effector.
• Staphylococcus aureus cadC, a transcription regulator of the cadmium resistance (cad) operon which encodes a Cd/Pb-specific efflux ATPase. CadC is responsive to Cd, Pb, Bi, and Zn ions.
• Mycobacterium tuberculosis nmtR, a Ni(II)/Co(II)-responsive repressor of the nmtA gene that encodes an ATPase exporter.

The signature pattern we developed starts one residue upstream of the helix-turn-helix motif and extends six residues upstream of its C-terminal extremity. We also developed a profile that covers the entire wHTH and which allows a more sensitive detection.