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P22495 (POLS_IPNVN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 59. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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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 N1) (IPNV)
Taxonomic identifier11004 [NCBI]
Taxonomic lineageViruses › dsRNA viruses › Birnaviridae › Aquabirnavirus ›
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 existenceInferred from homology

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 By similarity.

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 made 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 pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry By similarity.

Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing By similarity.

Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing By similarity.

Subunit structure

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

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. The 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 By similarity.

Sequence similarities

Contains 1 peptidase S50 domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 508508Precursor of VP2
PRO_0000392598
Chain1 – 442442Capsid protein VP2
PRO_0000036783
Peptide443 – 48644Structural peptide 1 By similarity
PRO_0000227862
Peptide487 – 4959Structural peptide 2 By similarity
PRO_0000227863
Peptide496 – 50813Structural peptide 3 By similarity
PRO_0000227864
Chain509 – 734226Protease VP4
PRO_0000036784
Chain735 – 972238Capsid protein VP3
PRO_0000036785

Regions

Domain509 – 734226Peptidase S50

Sites

Active site6331Nucleophile By similarity
Active site6741 By similarity
Metal binding261Divalent metal cation; shared with trimeric partners By similarity
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
Site715 – 7162Cleavage; by protease VP4; subsidiary By similarity
Site734 – 7352Cleavage; by protease VP4 By similarity

Sequences

Sequence LengthMass (Da)Tools
P22495 [UniParc].

Last modified August 1, 1991. Version 1.
Checksum: E59E9785616A2998

FASTA972106,670
        10         20         30         40         50         60 
MNTNKATATY LKSIMLPETG PASIPDDITE RHILKQETSS YNLEVSESGS GILVCFPGAP 

        70         80         90        100        110        120 
GSRIGAHYRW NANQTGLEFD QWLETSQDLK KAFNYGRLIS RKYDIQSSTL PAGLYALNGT 

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

       190        200        210        220        230        240 
TPQGLQSMNG AKMRCTAAIA PRRYEIDLPS QRLPPVPATG TLTTLYEGNA DIVNSTTVTG 

       250        260        270        280        290        300 
DINFSLAEQP ANETKFDFQL DFMGLDNDVP VVTVVSSVLA TNDNYRGVSA KMTQSIPTEN 

       310        320        330        340        350        360 
ITKPITRVKL SYKINQQTAI GNVATLGTMG PTTVSFSSGN GNVPGVLRPI TLVAYEKMTP 

       370        380        390        400        410        420 
LSILTVAGVS NYESYPNPEL LKNMVTRYGK YDPEGLNYAK MILSHREELD IRTVWRTEEY 

       430        440        450        460        470        480 
KERTRVFNEI TDFSSDLPTS KAWGWRDIVR GIRKVAAPVL STLFPMAAPL IGMADQFIGD 

       490        500        510        520        530        540 
LTKTNAAGGR YHSMAAGGRH KDVLESWASG GPDGKFSRAL KNRLESANYE EVELPPPSKG 

       550        560        570        580        590        600 
VIVPVVHTVK SAPGEAFGSL AIIIPGEYPE LLDANQQVLS HFANDTGSVW GIGEDIPFEG 

       610        620        630        640        650        660 
DNMCYTALPL KEIKRNGNIV VEKIFAGPIM GPSAQLGLSL LVNDIEDGVP RMVFTGEIAD 

       670        680        690        700        710        720 
DEETIIPICG VDIKAIAAHE PGLPLIGNQP GVDEEVRNTS LAAHLIQTGT LPVQRAKGSN 

       730        740        750        760        770        780 
KRIKYLGELM ASNASGMDEE LQRLLNATMA RAKEVQDAEI YKLLKLMAWT RKNDLTDHMY 

       790        800        810        820        830        840 
EWSKEDPDAL KFGKLISTPP KHPEKPKGPD QHHAQEARAT RISLDAVRAG ADFATPEWVA 

       850        860        870        880        890        900 
LNNYRGPSPG QFKYYLITGR EPEPGDEYED YIKQPIVKPT DMNKIRRLAN SVYGLPHQEP 

       910        920        930        940        950        960 
APEEFYDAVA AVFAQNGGRG PDQDQMQDLR ELARQMKRRP RNADAPRRTR APAEPAPPGR 

       970 
SRFTPSGDNA EV

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References

[1]"Sequence of the large double-stranded RNA segment of the N1 strain of infectious pancreatic necrosis virus: a comparison with other Birnaviridae."
Havarstein L.S., Kalland K.H., Christie K.E., Endresen C.
J. Gen. Virol. 71:299-308(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		D00701 Genomic RNA. Translation: BAA00609.1.
PIRGNXSN1. B34148.

3D structure databases

ProteinModelPortalP22495.
SMRP22495. Positions 514-716.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

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_IPNVN
AccessionPrimary (citable) accession number: P22495
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: April 3, 2013
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

SIMILARITY comments

Index of protein domains and families

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