Family

RNA-directed RNA polymerase, influenzavirus (IPR001009)

Short name: RNA-dir_pol_influenzavirus

Family relationships

None.

Description

RNA-directed RNA polymerase (RdRp) (EC:2.7.7.48) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [PMID: 2759231, PMID: 8709232]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [PMID: 11531403].

All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [PMID: 9309225]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [PMID: 10827187]. The domain organisation [PMID: 9878607] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.

There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:

  • Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.
  • Mononegavirales (negative-strand RNA viruses with non-segmented genomes).
  • Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.
  • Birnaviridae family of dsRNA viruses.
The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:
  • All positive-strand RNA eukaryotic viruses with no DNA stage.
  • All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).
  • Reoviridae family of dsRNA viruses.

The pattern describes the P2 subunit of Influenza RNA polymerase EC:2.7.7.48,an enzyme which is composed of three subunits: P1 (or PB1), P2 (or PA), and P3 (or PB2). The P2 subunit in addition to the P1 subunit is required for viral RNA synthesis in replication of the Influenza virus genome [PMID: 8709268].

GO terms

Biological Process

GO:0006351 transcription, DNA-templated

Molecular Function

GO:0003723 RNA binding
GO:0003968 RNA-directed RNA polymerase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
Pfam