PROSITE documentation PDOC51652

Nidoviruses zinc-binding (ZBD) domain profiles

Nidoviruses (Coronaviridae, Arteriviridae, and Roniviridae) feature the most complex genetic organization among plus-strand RNA viruses [E1,E2,E3]. Their replicase genes encode an exceptionally large number of nonstructural protein domains which mediate the key functions required for genomic RNA synthesis (replication) and subgenomic RNA (sgRNA) synthesis (transcription). They encode a nonstructural protein, called nsp10 in arteriviruses (AV) and nsp13 in coronaviruses (CV), that is comprised of a C-terminal nucleoside triphosphate-binding/helicase (Hel) motif and an N-terminal cysteine-rich zinc-binding domain (ZBD). The ZBD is critically involved in nidovirus replication and transcription by modulating the enzymatic activities of the helicase domain and other, yet unknown, mechanisms. The ZBD domain of nidovirus helicase is indispensable for its catalytic activity and the interplay between ZBD domain and core helicase domains is finely tuned [1,2,3,4,5].

The ZBD is comprised of about 80 to 100 residues, including 12 to 13 conserved Cys/His residues. It consists of a RING-like module and treble-cleft zinc finger, together coordinating three Zn atoms (see <PDB:4N0O>). The N-terminal RING-like module has a notable binuclear structure with a cross-brace topology involving 6 Cys and 2 His residues that coordinate two zinc ions. The C-terminal zinc finger of ZBD adopts a treble-cleft fold distinct from that of the RING module. It coordinates one Zn ion with a C[H/C]C[C/H] pattern [3,4,5].

The profiles we developed cover the entire AV and CV ZBD domains.