PROSITE documentation PDOC51753 [for PROSITE entry PS51753]

HBM domain profile

The helical bimodular (HBM) domain is a small molecule binding domain of around 250 amino acids. It is found in Bacteria and Archaea but is absent from eukaryotes and forms part of chemoreceptors (see <PDOC00465>) and histidine kinases (see <PDOC50109>). The HBM domain is composed of two structural modules, each of which recognizes a different type of ligand. The conservation of amino acids in the ligand binding sites of both modules suggests that HBM family members recognize similar ligands [1].

The HBM domain is composed of six helices linked by loops (see <PDB:2YFB>). Two short helices (α1 and α2) at the membrane-proximal part of the structure are followed by the long helix α3. This segment is followed by another couple of short helices (α4 and α5) and a second long helix α6, which is predicted to continue as a transmembrane helix. The structure can be understood as a duplication of a structural element made of two short and a long helix. The six helices of the HBM domain arrange into two modules, each forming a four-helix bundle. The membrane proximal module is composed of α1, α2, the N-terminal segment of α 3, and the C-terminal segment of α6. The membrane distal module is composed of the C-terminal segment of α3, helices α4 and α5, and the the N-terminal part of α6 [2].

The profile we developed covers the entire HBM domain.