Structure s and
proteomes of different families of nidoviruses Nidoviruses have a viral envelope and a positive-sense, single-stranded RNA genome which is capped and polyadenylated. The group expresses structural proteins separately from the nonstructural ones. The structural proteins are encoded at the 3' region of the
genome and are expressed from a set of
subgenomic mRNAs. Member viruses encode one main
proteinase and between one and three accessory proteinases which are mainly involved in expressing the
replicase gene. These proteinases are also responsible for activating or inactivating specific proteins at the correct time in the virus life cycle, ensuring replication occurs at the right time.
Genome Nidoviruses can be distinguished from other RNA viruses by a constellation of seven conserved domains—5'-TM2-3CLpro-TM3-RdRp-Zm-HEL1-NendoU-3'—with the first three being encoded in
ORF1a and the remaining four in
ORF1b. TM2 and TM3 and
transmembrane domains; RdRp is the
RNA-dependent RNA polymerase; Zm is a Zn-cluster binding domain fused with a
helicase (HEL1); 3CLpro is a
3C-like protease; and NendoU is an
uridylate-specific
endonuclease. The 3CLpro has a catalytic
His-
Cys dyad, and is related to the
SARS coronavirus main proteinase (Mpro). Most, but not all, nidovirus subgenomic RNAs contain a 5′ leader sequence derived from the 5′ end of the genomic RNA. The
frameshift that generates
ORF1b frameshift occurs at a
UUUAAAC heptanucleotide 'slippery' sequence located upstream of the ORF1a stop codon and a putative RNA
pseudoknot structure. Many proteins have been identified on the genomes of
Nidovirales, but their function has not yet been determined. Other enzymes that may be present in the genome include
papain-like proteases, ADP-ribose/poly(ADP-ribose)-binding or
ADP-ribose 1''-phosphate phosphatase activities and
cyclic nucleotide phosphodiesterase. == Phylogenetics ==