PROSITE documentation PDOC51657

(+)RNA virus helicase core domain profile

Helicases have been classified in 6 superfamilies (SF1-SF6) [1,2]. All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) (see <PDOC00017>) and Walker B (Mg2+-binding aspartic acid) motifs [1]. The two largest superfamilies, commonly referred to as SF1 and SF2 (see <PDOC51192>), share similar patterns of seven conserved sequence motifs, some of which are separated by long poorly conserved spacers [1]. Helicase motifs appear to be organized in a core domain which provides the catalytic function, whereas optional inserts and amino- and carboxy-terminal sequences may comprise distinct domains with diverse accessory roles. The helicase core contains two structural domains, an N-terminal ATP-binding domain and a C-terminal domain. Putative SF1 helicases are extremely widespread among positive-stranded (+)RNA viruses. They have been identified in a variety of plant virus families, as well as α- rubi-, arteri-, hepatitis E, and coronaviruses. A number of these viral enzymes have been implicated in diverse aspects of transcription and replication but also in RNA stability and cell-to-cell movement [3].

The (+)RNA virus helicase core contains two RecA-like α/β domains (see <PDB:3VKW>). The N-terminal ATP-binding domain contains a parallel six-stranded β-sheet surrounded by four helices on one side and two helices on the other. The C-terminal domain contains a parallel four-stranded β-sheet sandwiched between two helices on each of its sides. The (+)RNA virus helicase core is likely to bind NTP in cleft between the N-terminus of the ATP-binding domain and the beginning of the C-terminal domain [2].

The profile we developed covers the entire (+)RNA virus helicase core.