Summary: Birnavirus VP4 protein
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This is the Wikipedia entry entitled "Birnaviridae". More...
Birnaviridae Edit Wikipedia article
| Birnaviridae | |
|---|---|
Virus classification 
| |
| (unranked): | Virus |
| Realm: | Riboviria |
| Phylum: | incertae sedis |
| Family: | Birnaviridae |
| Genera | |
| Birnavirus RNA dependent RNA polymerase (VP1) | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Birna_RdRp | ||||||||
| Pfam | PF04197 | ||||||||
| InterPro | IPR007100 | ||||||||
| |||||||||
| Birnavirus VP2 protein | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 crystal structure of infectious bursal disease virus vp2 subviral particle | |||||||||
| Identifiers | |||||||||
| Symbol | Birna_VP2 | ||||||||
| Pfam | PF01766 | ||||||||
| Pfam clan | CL0055 | ||||||||
| InterPro | IPR002662 | ||||||||
| |||||||||
| Birnavirus VP3 protein | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Birna_VP3 | ||||||||
| Pfam | PF01767 | ||||||||
| InterPro | IPR002663 | ||||||||
| |||||||||
| Birnavirus VP4 protein | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Birna_VP4 | ||||||||
| Pfam | PF01768 | ||||||||
| InterPro | IPR002664 | ||||||||
| MEROPS | S50 | ||||||||
| |||||||||
| Birnavirus VP5 protein | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Birna_VP5 | ||||||||
| Pfam | PF03042 | ||||||||
| InterPro | IPR004284 | ||||||||
| |||||||||
Birnaviridae is a family of viruses[1]. Salmonid fish, young sexually immature chickens, and insects serve as natural hosts. There are currently six species in this family, divided among 4 genera.[2] 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.[2][3]
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.[4]
The large RNA segment, segment A, of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C) [5] 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.[5] VP4 protein is involved in generating VP2 and VP3.[5] recombinant VP3 is more immunogenic than recombinant VP2.[6]
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.[7][8] 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.[7]
Non structural protein VP5 is found in RNA segment A.[citation needed] 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.
Structure
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.[2][3]
| Genus | Structure | Symmetry | Capsid | Genomic arrangement | Genomic segmentation |
|---|---|---|---|---|---|
| Avibirnavirus | Icosahedral | T=13 | Non-enveloped | Linear | Segmented |
| Aquabirnavirus | Icosahedral | T=13 | Non-enveloped | Linear | Segmented |
| Blosnavirus | Icosahedral | T=13 | Non-enveloped | Linear | Segmented |
| Entomobirnavirus | Icosahedral | T=13 | Non-enveloped | Linear | Segmented |
Life cycle
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.[2][3]
| 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 |
Taxonomy
Group: dsRNA
- Family: Birnaviridae
References
- ^ Delmas, B; Attoui, H; Ghosh, S; Malik, YS; Mundt, E; Vakharia, VN; Ictv Report, Consortium (January 2019). "ICTV virus taxonomy profile: Birnaviridae". The Journal of General Virology. 100 (1): 5–6. doi:10.1099/jgv.0.001185. PMID 30484762.
- ^ a b c d e "Birnaviridae - Birnaviridae - dsRNA Viruses". International Committee on Taxonomy of Viruses (ICTV). Retrieved 16 October 2019.
- ^ a b c "Viral Zone". ExPASy. 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.
- ^ a b c 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 253673. 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. doi:10.1007/s00705-004-0339-2. PMID 15669113.
- ^ a b 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 VP4 protein Provide feedback
VP4 is a viral protease [1]. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C) [1].
Literature references
-
Jagadish MN, Staton VJ, Hudson PJ, Azad AA; , J Virol 1988;62:1084-1087.: Birnavirus precursor polyprotein is processed in Escherichia coli by its own virus-encoded polypeptide. PUBMED:2828658 EPMC:2828658
External database links
| MEROPS: | S50 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR025775
Viruses of the Birnaviridae family infect animal species belonging to vertebrates, molluscs, insects and rotifers and are characterised by their bi- segmented double-stranded RNA genome (segments A and B). Segment A encodes two overlapping reading frames and the larger open reading frame encodes a polyprotein (NH2-pVP2-VP4-VP3-COOH). The polyprotein is processed through the proteolytic activity of VP4 to generate pVP2 and VP3. During virus assembly pVP2 is further processed by VP4 to generate the capsid protein VP2 and structural peptides. Evolutionarily, the VP4 protease of the Birnaviridae family belongs to clan SJ and family S50 [PUBMED:10666235, PUBMED:16584747, PUBMED:17553791].
The birnavirus VP4 protease domain displays a catalytic serine/lysine dyad in its active site. The birnavirus VP4 protease domain has an alpha/beta fold [PUBMED:16584747, PUBMED:17553791].
Domain organisation
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| PP/heatmap | 1 | ||||||||
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Full (10) |
Representative proteomes | UniProt (825) |
NCBI (565) |
Meta (0) |
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RP35 (10) |
RP55 (10) |
RP75 (10) |
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
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Curation
| Seed source: | Pfam-B_946 (release 4.2) |
| Previous IDs: | none |
| Type: | Family |
| Sequence Ontology: | SO:0100021 |
| Author: |
Bateman A 
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| Number in seed: | 3 |
| Number in full: | 10 |
| Average length of the domain: | 273.80 aa |
| Average identity of full alignment: | 29 % |
| Average coverage of the sequence by the domain: | 26.87 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 259 | ||||||||||||
| Family (HMM) version: | 17 | ||||||||||||
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Species distribution
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Structures
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_VP4 domain has been found. There are 22 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 sequence.
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