Summary: Birnavirus RNA dependent RNA polymerase (VP1)
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Birnaviridae Edit Wikipedia article
|Group:||Group III (dsRNA)|
|Birnavirus RNA dependent RNA polymerase (VP1)|
|Birnavirus VP2 protein|
|crystal structure of infectious bursal disease virus vp2 subviral particle|
|Birnavirus VP3 protein|
|Birnavirus VP4 protein|
|Birnavirus VP5 protein|
The Birnaviridae are a family of viruses, including the following genera:
- Genus Aquabirnavirus; type species: Infectious pancreatic necrosis virus
- Genus Avibirnavirus; type species: Infectious bursal disease virus
- Genus Blosnavirus; type species: Blotched snakehead virus
- Genus Entomobirnavirus; type species: Drosophila X virus
The Birnaviridae genome encodes several proteins:
The Birnaviridae RNA-directed RNA polymerase (VP1), which lacks the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RNA-directed RNA polymerases.
The large RNA segment, segment A, of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C)  that is processed into the major structural proteins of the virion: VP2, VP3 (a minor structural component of the virus), and into the putative protease VP4. VP4 protein is involved in generating VP2 and VP3. recombinant VP3 is more immunogenic than recombinant VP2.
Infectious pancreatic necrosis virus (IPNV), a birnavirus, is an important pathogen in fish farms. Analyses of viral proteins showed that VP2 is the major structural and immunogenic polypeptide of the virus. All neutralizing monoclonal antibodies are specific to VP2 and bind to continuous or discontinuous epitopes. The variable domain of VP2 and the 20 adjacent amino acids of the conserved C-terminal are probably the most important in inducing an immune response for the protection of animals.
Non structural protein VP5 is found in RNA segment A. The function of this small viral protein is unknown. It is believed to be involved in influencing apoptosis, but studies are not completely concurring. The protein can not be found in the virion.
The family includes a number of viruses:
- Shwed PS, Dobos P, Cameron LA, Vakharia VN, Duncan R (May 2002). "Birnavirus VP1 proteins form a distinct subgroup of RNA-dependent RNA polymerases lacking a GDD motif". Virology 296 (2): 241â50. doi:10.1006/viro.2001.1334. PMID 12069523.
- Jagadish MN, Staton VJ, Hudson PJ, Azad AA (March 1988). "Birnavirus precursor polyprotein is processed in Escherichia coli by its own virus-encoded polypeptide". J. Virol. 62 (3): 1084â7. PMC 253673. PMID 2828658. //www.ncbi.nlm.nih.gov/pmc/articles/PMC253673/.
- Moon CH, Do JW, Cha SJ, Bang JD, Park MA, Yoo DJ, Lee JM, Kim HG, Chung DK, Park JW (October 2004). "Comparison of the immunogenicity of recombinant VP2 and VP3 of infectious pancreatic necrosis virus and marine birnavirus". Arch. Virol. 149 (10): 2059â68. PMID 15669113.
- Heppell J, Tarrab E, Lecomte J, Berthiaume L, Arella M (December 1995). "Strain variability and localization of important epitopes on the major structural protein (VP2) of infectious pancreatic necrosis virus". Virology 214 (1): 40â9. doi:10.1006/viro.1995.9956. PMID 8525637.
- Nobiron I, Galloux M, Henry C, Torhy C, Boudinot P, Lejal N, Da Costa B, Delmas B (February 2008). "Genome and polypeptides characterization of Tellina virus 1 reveals a fifth genetic cluster in the Birnaviridae family". Virology 371 (2): 350â61. doi:10.1016/j.virol.2007.09.022. PMID 17976679.
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Birnavirus RNA dependent RNA polymerase (VP1) Provide feedback
Birnaviruses are dsRNA viruses. This family corresponds to the RNA dependent RNA polymerase. This protein is also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps .
Shwed PS, Dobos P, Cameron LA, Vakharia VN, Duncan R; , Virology 2002;296:241-250.: Birnavirus VP1 Proteins Form a Distinct Subgroup of RNA-Dependent RNA Polymerases Lacking a GDD Motif. PUBMED:12069523 EPMC:12069523
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR007100
RNA-directed RNA polymerase (RdRp) (EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [PUBMED:2759231, PUBMED: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 [PUBMED: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 [PUBMED: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 [PUBMED:10827187]. The domain organisation [PUBMED: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.
- 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 family consists of the Birnaviridae enzymes. These proteins lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RNA-directed RNA polymerases [PUBMED:12069523].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||RNA-directed RNA polymerase activity (GO:0003968)|
|Biological process||viral genome replication (GO:0019079)|
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Curation and family details
|Seed source:||Pfam-B_2204 (release 7.3)|
|Number in seed:||5|
|Number in full:||338|
|Average length of the domain:||401.50 aa|
|Average identity of full alignment:||68 %|
|Average coverage of the sequence by the domain:||97.83 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Birna_RdRp domain has been found. There are 27 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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