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|
Birnaviridae is a family of viruses. Salmonid fish, young sexually immature chickens, and insects serve as natural hosts. There are currently six species in this family, divided among 4 genera. Diseases associated with this family include: IPNV: infectious pancreatic necrosis in salmonid fish, causes significant losses to the aquaculture industry. chronic infection in adult, and acute viral disease in young salmonid fish.
The Birnaviridae genome encodes several proteins:
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.
Viruses in Birnaviridae are non-enveloped, with icosahedral and Single-shelled geometries, and T=13 symmetry. The diameter is around 70 nm. Genomes are linear and segmented, around 15.2.3-3kb in length. The genome codes for 5 to 6 proteins.
|Genus||Structure||Symmetry||Capsid||Genomic arrangement||Genomic segmentation|
Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the double-stranded RNA virus replication model. Double-stranded rna virus transcription is the method of transcription. Salmonid fish, young sexually immature chickens, and insects serve as the natural host. Transmission routes are contact.
|Genus||Host details||Tissue tropism||Entry details||Release details||Replication site||Assembly site||Transmission|
|Avibirnavirus||Birds||None||Cell receptor endocytosis||Budding||Cytoplasm||Cytoplasm||Contact|
|Aquabirnavirus||Salmonid fish||None||Cell receptor endocytosis||Budding||Cytoplasm||Cytoplasm||Contact|
|Blosnavirus||Blotched snakehead fish||None||Unknown||Budding||Cytoplasm||Cytoplasm||Unknown|
|Entomobirnavirus||Insects: diptera||None||Cell receptor endocytosis||Budding||Cytoplasm||Cytoplasm||Unknown|
- "Viral Zone". ExPASy. Retrieved 12 June 2015.
- ICTV. "Virus Taxonomy: 2014 Release". Retrieved 12 June 2015.
- 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): 241–250. 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): 1084–7. PMC . PMID 2828658.
- 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): 2059–68. 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): 40–9. 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): 350–61. 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
Internal database links
|Similarity to PfamA using HHSearch:||RdRP_1|
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)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This clan represents the replicative RNA dependent RNA polymerase. from a variety of RNA viruses .
The clan contains the following 10 members:Birna_RdRp Flavi_NS5 Mitovir_RNA_pol RdRP_1 RdRP_2 RdRP_3 RdRP_4 RVT_1 RVT_2 Viral_RdRp_C
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Key: available, not generated, — not available.
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|Seed source:||Pfam-B_2204 (release 7.3)|
|Number in seed:||3|
|Number in full:||4|
|Average length of the domain:||834.80 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||93.06 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 30 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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