Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156
This domain family contains an uncharacterized protein YrkD from Bacillus subtilis and related proteins. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved, there is an Asn instead of the His (C-N-C); also a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are very poorly conserved.
Feature 1:putative metal binding site [ion binding site]
Evidence:
Comment:based on the binding of another superfamily member (Mycobacterium tuberculosis CsoR/MtCsoR) to Cu(I)
Comment:not all members of this superfamily are responsive to metal ions
Comment:MtCsoR forms a homotetramer (dimer of dimers); each CsoR homodimer contains two symmetry-related subunit-bridging Cu(I) binding sites, one on either end. Each Cu(I) is coordinated by a Cys residue from one monomer, and a His and Cys residue from its partner monomer. In this family, however, not all these residues are conserved, the His residue is an Asn
Jiyao W et al.(2023). "The conserved domain database in 2023.",