Protein Domain : IPR007094

Type:  Domain Name:  RNA-directed RNA polymerase, catalytic domain
Description:  RNA-directed RNA polymerase (RdRp) () is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. 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 []. 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 []. 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 [].The domain organisation [] 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.This entry represents the catalytic domain of the RNA-directed RNA polymerase from all positive-strand RNA eukaryotic viruses with no DNA stage. Short Name:  RNA-dir_pol_PSvirus
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0 Child Features

0 Contains

1 Cross References

Identifier
PS50507

3 Found Ins

DB identifier Type Name
IPR014412 Family Genome polyprotein, Flavivirus
IPR000208 Domain RNA-directed RNA polymerase, flavivirus
IPR001788 Domain Tymovirus, RNA-dependent RNA polymerase

2 GO Annotations

GO Term Gene Name
GO:0003968 IPR007094
GO:0039694 IPR007094

2 Ontology Annotations

GO Term Gene Name
GO:0003968 IPR007094
GO:0039694 IPR007094

0 Parent Features

3 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
Potri.006G051400.1 A0A2K1ZX22 PAC:27006393 Populus trichocarpa 381  
Potri.006G051400.1.p A0A2K1ZX22 PAC:37241865 Populus trichocarpa 381  
HORVU7Hr1G022460.1 PAC:38541838 Hordeum vulgare 47  

6 Publications

First Author Title Year Journal Volume Pages PubMed ID
            9878607
            9309225
            2759231
            10827187
            8709232
            11531403