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P05844 (POLS_IPNVJ) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 74. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Structural polyprotein

Short name=PP

Cleaved into the following 7 chains:

  1. Precursor of VP2
    Short name=Pre-VP2
  2. Capsid protein VP2
  3. Structural peptide 1
    Short name=p1
  4. Structural peptide 2
    Short name=p2
  5. Structural peptide 3
    Short name=p3
  6. Protease VP4
    EC=3.4.21.-
    Alternative name(s):
    Non-structural protein VP4
    Short name=NS
  7. Capsid protein VP3
OrganismInfectious pancreatic necrosis virus (strain Jasper) (IPNV) [Reference proteome]
Taxonomic identifier11003 [NCBI]
Taxonomic lineageVirusesdsRNA virusesBirnaviridaeAquabirnavirus
Virus hostOncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) [TaxID: 8022]
Salmo [TaxID: 8028]

Protein attributes

Sequence length972 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell.

The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures By similarity.

Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation By similarity.

Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid composed of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator By similarity.

Structural peptide 1 is a small peptide derived from the C-terminus of pre-VP2. It destabilizes and perforates cell membranes, suggesting a role during viral entry By similarity.

Structural peptide 2 is a small peptide derived from the C-terminus of pre-VP2. It is not essential for virus viability, but viral growth is affected when this protein is absent By similarity.

Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for virus viability, but viral growth is affected when this protein is absent By similarity.

Subunit structure

Capsid protein VP2 is a homotrimer. A central divalent metal (possibly cobalt) stabilizes the VP2 trimer. Capsid protein VP3 is a homodimer. Capsid protein VP3 interacts (via C-terminus) with VP1 in the cytoplasm. Capsid protein VP3 interacts with VP2 By similarity. Ref.3

Subcellular location

Capsid protein VP2: Virion Potential. Host cytoplasm Potential.

Capsid protein VP3: Virion Potential. Host cytoplasm Potential.

Structural peptide 1: Virion Potential. Host cytoplasm Potential.

Structural peptide 2: Virion Potential. Host cytoplasm Potential.

Structural peptide 3: Virion Potential. Host cytoplasm Potential.

Post-translational modification

Specific enzymatic cleavages yield mature proteins. Capsid assembly seems to be regulated by polyprotein processing. The protease VP4 cleaves itself off the polyprotein, thus releasing pre-VP2 and VP3 within the infected cell. During capsid assembly, the C-terminus of pre-VP2 is further processed by VP4, giving rise to VP2, the external capsid protein and three small peptides that all stay closely associated with the capsid.

Sequence similarities

Contains 1 peptidase S50 domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 972972Structural polyprotein
PRO_0000391632
Chain1 – 508508Precursor of VP2
PRO_0000391633
Chain1 – 442442Capsid protein VP2
PRO_0000036780
Peptide443 – 48644Structural peptide 1 By similarity
PRO_0000227859
Peptide487 – 4959Structural peptide 2 By similarity
PRO_0000227860
Peptide496 – 50813Structural peptide 3 By similarity
PRO_0000227861
Chain509 – 734226Protease VP4
PRO_0000036781
Chain735 – 972238Capsid protein VP3
PRO_0000036782

Regions

Domain509 – 734226Peptidase S50

Sites

Active site6331Nucleophile By similarity
Active site6741 By similarity
Metal binding261Divalent metal cation; shared with trimeric partners
Site442 – 4432Cleavage; by protease VP4 By similarity
Site486 – 4872Cleavage; by protease VP4 By similarity
Site495 – 4962Cleavage; by protease VP4 By similarity
Site508 – 5092Cleavage; by protease VP4 By similarity
Site734 – 7352Cleavage; by protease VP4 By similarity

Secondary structure

... 972
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P05844 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: 5CABCD0414EE122B

FASTA972106,666
        10         20         30         40         50         60 
MSTSKATATY LRSIMLPENG PASIPDDITE RHILKQETSS YNLEVSESGS GLLVCFPGAP 

        70         80         90        100        110        120 
GSRVGAHYRW NLNQTALEFD QWLETSQDLK KAFNYGRLIS RKYDIQSSTL PAGLYALNGT 

       130        140        150        160        170        180 
LNAATFEGSL SEVESLTYNS LMSLTTNPQD KVNNQLVTKG ITVLNLPTGF DKPYVRLEDE 

       190        200        210        220        230        240 
TPQGPQSMNG ARMRCTAAIA PRRYEIDLPS ERLPTVAATG TPTTIYEGNA DIVNSTAVTG 

       250        260        270        280        290        300 
DITFQLEAEP VNETRFDFIL QFLGLDNDVP VVTVTSSTLV TADNYRGASA KFTQSIPTEM 

       310        320        330        340        350        360 
ITKPITRVKL AYQLNQQTAI ANAATLGAKG PASVSFSSGN GNVPGVLRPI TLVAYEKMTP 

       370        380        390        400        410        420 
QSILTVAGVS NYELIPNPDL LKNMVTKYGK YDPEGLNYAK MILSHREELD IRTVWRTEEY 

       430        440        450        460        470        480 
KERTRAFKEI TDFTSDLPTS KAWGWRDLVR GIRKVAAPVL STLFPMAAPL IGAADQFIGD 

       490        500        510        520        530        540 
LTKTNSAGGR YLSHAAGGRY HDVMDSWASG SEAGSYSKHL KTRLESNNYE EVELPKPTKG 

       550        560        570        580        590        600 
VIFPVVHTVE SAPGEAFGSL VVVIPEAYPE LLDPNQQVLS YFKNDTGCVW GIGEDIPFEG 

       610        620        630        640        650        660 
DDMCYTALPL KEIKRNGNIV VEKIFAGPAM GPSSQLALSL LVNDIDEGIP RMVFTGEIAD 

       670        680        690        700        710        720 
DEETVIPICG VDIKAIAAHE HGLPLIGCQP GVDEMVANTS LASHLIQGGA LPVQKAQGAC 

       730        740        750        760        770        780 
RRIKYLGQLM RTTASGMDAE LQGLLQATMA RAKEVKDAEV FKLLKLMSWT RKNDLTDHMY 

       790        800        810        820        830        840 
EWSKEDPDAI KFGRLVSTPP KHQEKPKGPD QHTAQEAKAT RISLDAVKAG ADFASPEWIA 

       850        860        870        880        890        900 
ENNYRGPSPG QFKYYMITGR VPNPGEEYED YVRKPITRPT DMDKIRRLAN SVYGLPHQEP 

       910        920        930        940        950        960 
APDDFYQAVV EVFAENGGRG PDQDQMQDLR DLARQMKRRP RPAETRRQTK TPPRAATSSG 

       970 
SRFTPSGDDG EV 

« Hide

References

[1]"The nucleotide sequence of infectious pancreatic necrosis virus (IPNV) dsRNA segment A reveals one large ORF encoding a precursor polyprotein."
Duncan R., Dobos P.
Nucleic Acids Res. 14:5934-5934(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"Synthesis of the infectious pancreatic necrosis virus polyprotein, detection of a virus-encoded protease, and fine structure mapping of genome segment A coding regions."
Duncan R., Nagy E., Krell P.J., Dobos P.
J. Virol. 61:3655-3664(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 433-972, SEQUENCE REVISION TO 566 AND 708.
[3]"Crystal structure of an aquabirnavirus particle: insights into antigenic diversity and virulence determinism."
Coulibaly F., Chevalier C., Delmas B., Rey F.A.
J. Virol. 84:1792-1799(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, STRUCTURE BY ELECTRON MICROSCOPY (3.4 ANGSTROMS) OF SUBVIRAL PARTICLES.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M18049 Genomic RNA. Translation: AAA89179.1.
PIRGNXSIV. A23599.
T09624.
RefSeqNP_047196.1. NC_001915.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZEDX-ray2.20D/E/F733-972[»]
ProteinModelPortalP05844.
SMRP05844. Positions 514-716.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID956513.

Family and domain databases

InterProIPR002662. Birna_VP2.
IPR002663. Birna_VP3.
IPR025775. Birna_VP4_Prtase_dom.
[Graphical view]
PfamPF01766. Birna_VP2. 1 hit.
PF01767. Birna_VP3. 1 hit.
PF01768. Birna_VP4. 1 hit.
[Graphical view]
PROSITEPS51548. BIRNAVIRUS_VP4_PRO. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLS_IPNVJ
AccessionPrimary (citable) accession number: P05844
Secondary accession number(s): Q82720
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: May 30, 2000
Last modified: May 1, 2013
This is version 74 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references