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Q703G9 (POLS_IPNVS) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 50. 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 Sp) (IPNV) [Complete proteome]
Taxonomic identifier11005 [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 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.

Miscellaneous

The sequence shown is that of strain 31-75. Isolate Sp103 is VP5-deficient.

Sequence similarities

Contains 1 peptidase S50 domain.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 508508Precursor of VP2
PRO_0000392599
Chain1 – 442442Capsid protein VP2
PRO_0000227873
Peptide443 – 48644Structural peptide 1
PRO_0000227874
Peptide487 – 4959Structural peptide 2
PRO_0000227875
Peptide496 – 50813Structural peptide 3
PRO_0000227876
Chain509 – 734226Protease VP4
PRO_0000227877
Chain735 – 972238Capsid protein VP3
PRO_0000227878

Regions

Domain509 – 734226Peptidase S50

Sites

Active site6331Nucleophile Ref.9
Active site6741 Ref.9
Metal binding261Divalent metal cation; shared with trimeric partners By similarity
Site442 – 4432Cleavage; by protease VP4
Site486 – 4872Cleavage; by protease VP4
Site495 – 4962Cleavage; by protease VP4
Site508 – 5092Cleavage; by protease VP4
Site715 – 7162Cleavage; by protease VP4; subsidiary
Site734 – 7352Cleavage; by protease VP4

Natural variations

Natural variant361Q → P in strain: Isolate Mason.
Natural variant461S → P in strain: Isolate Mason.
Natural variant521V → I in strain: Isolate Mason, Isolate Tseng, Isolate Blake, Isolate Sp103, Isolate Sp116, Isolate Sp122, Isolate NVI-001, Isolate NVI-011, Isolate NVI-013, Isolate NVI-015, Isolate NVI-016, Isolate NVI-020 and NVI-023.
Natural variant541V → I in strain: Isolate NVI-010.
Natural variant82 – 854WLET → CWRA in strain: Isolate Mason.
Natural variant1521V → A in strain: Isolate Mason, Isolate Blake and Isolate Tseng.
Natural variant1921K → R in strain: Isolate Mason, Isolate Blake and Isolate Tseng.
Natural variant1991I → T in strain: Isolate Sp103 and Isolate Sp122.
Natural variant2121R → S in strain: Isolate Mason, Isolate Blake and Isolate Tseng.
Natural variant2171P → T in strain: Isolate Sp122, Isolate NVI-001, Isolate NVI-011, Isolate NVI-013, Isolate NVI-015, Isolate NVI-020 and Isolate NVI-023.
Natural variant2191T → I in strain: Isolate NVI-010.
Natural variant2211T → A in strain: Isolate NVI-001, Isolate NVI-013, Isolate NVI-015, Isolate Sp116 and Isolate NVI-023.
Natural variant2221L → P in strain: Isolate NVI-011.
Natural variant2341N → S in strain: Isolate Tseng.
Natural variant2471A → T in strain: Isolate Sp122, Isolate NVI-001, Isolate NVI-013, Isolate NVI-015 and Isolate NVI-023.
Natural variant2491Q → R in strain: Isolate Tseng.
Natural variant2521D → N in strain: Isolate Mason, Isolate Tseng, Isolate Blake, Isolate Sp103, Isolate NVI-010 and Isolate NVI-016.
Natural variant2521D → V in strain: Isolate NVI-001, Isolate NVI-011, Isolate NVI-013, Isolate NVI-015, Isolate NVI-020, Isolate NVI-023, Isolate Sp116 and Isolate Sp122.
Natural variant2551K → R in strain: Isolate Mason, Isolate Blake and Isolate Tseng.
Natural variant2621F → L in strain: Isolate Mason.
Natural variant2881V → A in strain: Isolate Sp116.
Natural variant3191A → E in strain: Isolate NVI-016.
Natural variant3231V → A in strain: Isolate NVI-020.
Natural variant3231V → F in strain: Isolate NVI-016.
Natural variant432 – 4343DFS → EKT in strain: Isolate Mason.
Natural variant4551V → I in strain: Isolate Mason.
Natural variant4731M → T in strain: Isolate Mason, Isolate Heppel and Isolate Blake.
Natural variant5001Y → H in strain: Isolate Heppel, Isolate NVI-010, Isolate NVI-011, Isolate NVI-020, Isolate Sp103 and Isolate Sp116.
Natural variant5651P → R in strain: Isolate Mason.
Natural variant570 – 5712EL → SF in strain: Isolate Mason.
Natural variant6721D → A in strain: Isolate NVI-016.
Natural variant7171K → Q in strain: Isolate NVI-016.
Natural variant7881D → G in strain: Isolate NVI-011.
Natural variant7881D → Y in strain: Isolate NVI-001.
Natural variant8021H → R in strain: Isolate NVI-015 and Isolate NVI-016.
Natural variant8411L → M in strain: Isolate NVI-016.
Natural variant8671E → Q in strain: Isolate Mason and Isolate Blake.
Natural variant8751P → S in strain: Isolate NVI-016.
Natural variant8821M → T in strain: Isolate Tseng.
Natural variant953 – 9542AE → GK in strain: Isolate Mason.
Natural variant959 – 9602GR → DV in strain: Isolate Mason.
Natural variant9681D → N in strain: Isolate Sp116.

Experimental info

Mutagenesis508 – 5092AS → QL: Complete loss of pVP2-VP4 cleavage.
Mutagenesis5471H → S: Strongly reduced VP4-VP3 cleavage. No effect on pVP2-VP4 cleavage. Ref.9
Mutagenesis5731D → Q: No effect on polyprotein processing. Ref.9
Mutagenesis5851D → I: No effect on polyprotein processing. Ref.9
Mutagenesis5951D → L: No effect on polyprotein processing. Ref.9
Mutagenesis6011D → S: No effect on polyprotein processing. Ref.9
Mutagenesis6331S → A, Q or T: Complete loss of protease activity. Ref.9
Mutagenesis6331S → C: Partial loss of protease activity. Ref.9
Mutagenesis6441D → I: No effect on polyprotein processing. Ref.9
Mutagenesis660 – 6612DD → GS: No effect on polyprotein processing.
Mutagenesis6721D → N: No effect on polyprotein processing. Ref.9
Mutagenesis6741K → A, D, H, Q or R: Complete loss of protease activity. Ref.9
Mutagenesis6751A → D: 60% loss of pVP2-VP4 and VP4-VP3 cleavages. Ref.9
Mutagenesis6761I → A: No effect on polyprotein processing. Ref.9
Mutagenesis6771A → D: 60% loss of pVP2-VP4. Complete loss of VP4-VP3 cleavage. Ref.9
Mutagenesis6781A → S: No effect on polyprotein processing. Ref.9
Mutagenesis6791H → L: Strongly reduced VP4-VP3 cleavage. No effect on pVP2-VP4 cleavage. Ref.9
Mutagenesis6801E → M: No effect on polyprotein processing. Ref.9
Mutagenesis6821G → L: No effect on polyprotein processing. Ref.9
Mutagenesis6831L → A: 60% loss of pVP2-VP4 and VP4-VP3 cleavages. Ref.9
Mutagenesis6841P → Q: No effect on polyprotein processing. Ref.9
Mutagenesis6851L → A: 60% loss of pVP2-VP4 and VP4-VP3 cleavages. Ref.9
Mutagenesis6861I → A: 20% loss of pVP2-VP4 and VP4-VP3 cleavages. Ref.9
Mutagenesis6871G → A: 20% loss of pVP2-VP4 and VP4-VP3 cleavages. Ref.9
Mutagenesis6891Q → I: No effect on polyprotein processing. Ref.9
Mutagenesis6931D → L: Strongly reduced VP4-VP3 cleavage. No effect on pVP2-VP4 cleavage. Ref.9
Mutagenesis7041H → S: No effect on polyprotein processing. Ref.9
Mutagenesis734 – 7352AS → LE: Complete loss of VP4-VP3 cleavage.
Sequence conflict8831N → Y in AAR10446. Ref.5

Secondary structure

........................................................................ 972
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q703G9 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 7B1448E99800E3C9

FASTA972106,646
        10         20         30         40         50         60 
MNTNKATATY LKSIMLPETG PASIPDDITE RHILKQETSS YNLEVSESGS GVLVCFPGAP 

        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 ADETKFDFQL DFMGLDNDVP VVTVVSSVLA TNDNYRGVSA KMTQSIPTEN 

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

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

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

       490        500        510        520        530        540 
LTKTNAAGGR YHSMAAGGRY 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 QGLPLIGNQP 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 

« Hide

References

[1]"Peptides resulting from the pVP2 C-terminal processing are present in infectious pancreatic necrosis virus particles."
Galloux M., Chevalier C., Henry C., Huet J.-C., Da Costa B., Delmas B.
J. Gen. Virol. 85:2231-2236(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], PROTEIN SEQUENCE OF 443-457; 487-495 AND 496-508, PROTEOLYTIC PROCESSING OF POLYPROTEIN.
Strain: 31-75.
[2]Mason C.L., Leong J.C.
Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Isolate Mason.
[3]Tseng C.-C., Lo C.-F., Kou G.-H.
Submitted (APR-1996) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Isolate Tseng.
[4]"Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus."
Santi N., Vakharia V.N., Evensen O.
Virology 322:31-40(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Isolate NVI-001, Isolate NVI-010, Isolate NVI-011, Isolate NVI-013, Isolate NVI-015, Isolate NVI-016, Isolate NVI-020 and Isolate NVI-023.
[5]"Molecular characterization of Sp serotype strains of infectious pancreatic necrosis virus exhibiting differences in virulence."
Shivappa R.B., Song H., Yao K., Aas-Eng A., Evensen O., Vakharia V.N.
Dis. Aquat. Organ. 61:23-32(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Isolate Sp103, Isolate Sp116 and Isolate Sp122.
[6]"Infectious pancreatic necrosis virus VP5 is dispensable for virulence and persistence."
Santi N., Song H., Vakharia V.N., Evensen O.
J. Virol. 79:9206-9216(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Isolate Sp103.
[7]"Phylogenetic relationships of aquatic birnaviruses based on deduced amino acid sequences of genome segment A cDNA."
Blake S., Ma J.Y., Caporale D.A., Jairath S., Nicholson B.L.
Dis. Aquat. Organ. 45:89-102(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-968.
Strain: Isolate Blake.
[8]"Comparison of amino acid sequences deduced from a cDNA fragment obtained from infectious pancreatic necrosis virus (IPNV) strains of different serotypes."
Heppell J., Berthiaume L., Corbin F., Tarrab E., Lecomte J., Arella M.
Virology 195:840-844(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 437-539.
Strain: Isolate Heppell.
[9]"Active residues and viral substrate cleavage sites of the protease of the birnavirus infectious pancreatic necrosis virus."
Petit S., Lejal N., Huet J.-C., Delmas B.
J. Virol. 74:2057-2066(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 509-515; 716-723 AND 735-740, ACTIVE SITES OF PROTEASE VP4, PROTEOLYTIC PROCESSING OF POLYPROTEIN, MUTAGENESIS OF 486-ALA-ALA-487; 495-ALA-ALA-496; 508-ALA-SER-509; HIS-547; ASP-573; ASP-585; ASP-595; ASP-601; SER-633; ASP-644; 660-ASP-ASP-661; ASP-672; LYS-674; ALA-675; ILE-676; ALA-677; ALA-678; HIS-679; GLU-680; GLY-682; LEU-683; PRO-684; LEU-685; ILE-686; GLY-687; GLN-689; ASP-693; HIS-704 AND 734-ALA-SER-735.
Strain: 31-75.
[10]"Structure of birnavirus-like particles determined by combined electron cryomicroscopy and X-ray crystallography."
Pous J., Chevalier C., Ouldali M., Navaza J., Delmas B., Lepault J.
J. Gen. Virol. 86:2339-2346(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING, ELECTRON MICROSCOPY (15 ANGSTROMS) OF VIRAL PARTICLES.
Strain: 31-75.
[11]"Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction."
Lee J., Feldman A.R., Delmas B., Paetzel M.
J. Biol. Chem. 282:24928-24937(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) OF 514-716.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ622822 Genomic RNA. Translation: CAF22217.1.
U48225 Genomic RNA. Translation: AAD11535.1.
U56907 Genomic RNA. Translation: AAB39512.1.
AY374435 Genomic RNA. Translation: AAQ75364.1.
AY379735 Genomic RNA. Translation: AAQ75348.1.
AY379736 Genomic RNA. Translation: AAQ75350.1.
AY379737 Genomic RNA. Translation: AAQ75352.1.
AY379738 Genomic RNA. Translation: AAQ75354.1.
AY379740 Genomic RNA. Translation: AAQ75357.1.
AY379742 Genomic RNA. Translation: AAQ75360.1.
AY379744 Genomic RNA. Translation: AAQ75363.1.
AY354519 Genomic RNA. Translation: AAR10446.1.
AY354520 Genomic RNA. Translation: AAR10449.1.
AY354521 Genomic RNA. Translation: AAR10452.1.
AY823632 Genomic RNA. Translation: AAX24140.1.
AF342728 mRNA. Translation: AAK32154.1.
L13988 Genomic RNA. Translation: AAB00986.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2PNLX-ray2.21A/B/C/D/E/F/G/H/I/J514-716[»]
2PNMX-ray2.30A524-716[»]
3IDEX-ray3.35A/B/C/D/E1-442[»]
ProteinModelPortalQ703G9.
SMRQ703G9. Positions 514-716.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSS50.001.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D2.60.120.20. 2 hits.
InterProIPR002662. Birna_VP2.
IPR002663. Birna_VP3.
IPR025775. Birna_VP4_Prtase_dom.
IPR029053. Viral_coat.
[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...

Other

EvolutionaryTraceQ703G9.

Entry information

Entry namePOLS_IPNVS
AccessionPrimary (citable) accession number: Q703G9
Secondary accession number(s): P90205 expand/collapse secondary AC list , Q4KTX8, Q69CH7, Q69CI0, Q69CI3, Q6U2N3, Q6U2N5, Q6U2N8, Q6U2P1, Q6U2P5, Q6U2P7, Q6UAY7, Q82733, Q990Q0, Q9YJV0
Entry history
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: July 5, 2004
Last modified: July 9, 2014
This is version 50 of the entry and version 1 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