Protein | Function | Virus groups | Homologs in cellular life forms | Comments | References |
---|---|---|---|---|---|
Jelly-roll capsid protein (JRC) | Main capsid subunit of icosahedral virions | Picornaviruses, comoviruses, carmoviruses, dsRNA phage, NCLDV, herpesviruses, adenoviruses, papovaviruses, parvoviruses, icosahedral DNA phages and archaeal viruses | Distinct jelly-roll domains are seen in eukaryotic nucleoplasmins and in protein-protein interaction domains of certain enzymes | Certain icosahedral viruses, such as ssRNA phages and alphaviruses, have unrelated capsid proteins. In poxviruses, the JRC is not a virion protein but forms intermediate structures during virion morphogenesis | [13–15, 53, 54, 109–111] |
Superfamily 3 helicase (S3H) | Initiation and elongation of genome replication | Picornaviruses, comoviruses, eukaryotic RCR viruses, NCLDV, baculoviruses, some phages (e.g., P4), plasmids, particularly, archaeal ones | S3H is a distinct, deep-branching family of the AAA+ ATPase class | Characteristic fusion with primase in DNA viruses and plasmids | [16, 112] |
Archaeo-eukaryotic DNA primase | Initiation of genome replication | NCLDV, herpesviruses, baculoviruses, some phages | All viral primases appear to form a clade within the archaeo-eukaryotic primase family | Characteristic fusion with S3H in most NCLDV, some phages, and archaeal plasmids | [18] |
UL9-like superfamily 2 helicase | Initiation and elongation of genome replication | Herpesviruses, some NCLDV, some phages | Viral UL9-like helicases form a distinct branch in the vast superfamily of DNA and RNA helicases | Fusion with primase in asfarviruses, mimiviruses | [53] |
Rolling-circle replication initiation endonuclease (RCRE)/origin-binding protein | Initiation of genome replication | Small eukaryotic DNA viruses (parvo-, gemini-, circo-, papova), phages, plasmids, and eukaryotic helitron transposons | No cellular RCRE or papovavirus-type origin-binding protein; however, these proteins have a derived form of the palm domain that is found in the majority of cellular DNA polymerases | Papovaviruses have an inactivated form of RCRE that functions as origin-binding protein | [17–20] |
Packaging ATPase of the FtsK family | DNA packaging into the virion | NCLDV, adenoviruses, polydnaviruses, some phages (e.g., P9, M13), nematode transposons | A distinct clade in the FtsK/HerA superfamily of P-loop NTPases that includes DNA-pumping ATPases of bacteria and archaea | Â | [113] |
ATPase subunit of terminase | DNA packaging into the virion | Herpesviruses, tailed phages | The terminases comprise a derived family of P-loop NTPases that is distantly related to Superfamily I/II helicases and AAA+ ATPases | Â | [109, 114] |
RNA-dependent RNA polymerase (RdRp)/reverse transcriptase (RT) | Replication of RNA genomes | Positive-strand RNA viruses, dsRNA viruses, retroid viruses/elements, possibly, negative-strand RNA viruses | Another major group of palm domains that are distinct from those in DNA polymerases | The RdRps of dsRNA viruses are homologs of positive-strand RNA virus polymerases. The provenance of negative-strand RNA virus RdRp remains uncertain although sequence motif and, especially, structural analysis suggests their derivation from positive-strand RNA virus RdRps | [23–25, 28, 87, 115] |