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Protein

Structural polyprotein

Gene
N/A
Organism
Yellowtail ascites virus - Y-6
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation
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.UniRule annotation
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.UniRule annotation
Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry.UniRule annotation
Structural peptide 2 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing.UniRule annotation
Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing.UniRule annotation
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.UniRule annotation

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine proteaseUniRule annotation

Keywords - Ligandi

Metal-bindingUniRule annotation

Protein family/group databases

MEROPSiS50.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Structural polyproteinUniRule annotation (EC:3.4.21.-UniRule annotation)
Short name:
PPUniRule annotation
OrganismiYellowtail ascites virus - Y-6Imported
Taxonomic identifieri360000 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesBirnaviridaeAquabirnavirus

Subcellular locationi

  • Host cytoplasm UniRule annotation
  • Virion UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid proteinUniRule annotation, Host cytoplasmUniRule annotation, Virion

PTM / Processingi

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi588 ↔ 604Combined sources

Interactioni

Subunit structurei

Capsid protein VP2 is a homotrimer. A central divalent metal stabilizes the VP2 trimer.UniRule annotation
Capsid protein VP3 is a homodimer.UniRule annotation

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IZJX-ray2.50A/B/C/D/E508-716[»]
4IZKX-ray2.30A/B508-716[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini509 – 734226Peptidase S50InterPro annotationAdd
BLAST

Sequence similaritiesi

Contains 1 peptidase S50 domain.UniRule annotation

Family and domain databases

Gene3Di2.60.120.20. 2 hits.
InterProiIPR002662. Birna_VP2.
IPR002663. Birna_VP3.
IPR025775. Birna_VP4_Prtase_dom.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF01766. Birna_VP2. 1 hit.
PF01767. Birna_VP3. 1 hit.
PF01768. Birna_VP4. 1 hit.
[Graphical view]
PROSITEiPS51548. BIRNAVIRUS_VP4_PRO. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P89521-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNTTKATATY LRSIMLPENG PASIPDDITE RHILKQETSS YNLEVSDSGS
60 70 80 90 100
GLLVCFPGAP GSRVGAHYKW NQNQTELEFD QWLETSQDLK KAFNYGRLIS
110 120 130 140 150
RKYDVQSSTL PAGLYALNGT LNAATFEGSL SEVESFSYNS LMSLTTNPQD
160 170 180 190 200
KVNNQLVTKG VTVLNLPTGF DKPYVRLEDE TPQGPQSMNG ARMRCTAAIA
210 220 230 240 250
PRRYEIDLPS ARLPTVPATG TLTTIYEGNA DIVNSTTVTG DISFRLEQDP
260 270 280 290 300
PNDTKYDFQL DFLGLDNNVP VVSITSSTLA TTDNYRGVSV KFTQSIPTET
310 320 330 340 350
ITKPITRVKL SYKINQQTAI GNAATLGPLG PSSVSFSSGN GNVPGVLRPI
360 370 380 390 400
TLVAYEKMTP QSILTVAGVS NYELIPNPEL LKNMVTKYGK YDPEGLNYAK
410 420 430 440 450
MILSHREELD IRTVWRTEEY KERTRAFNEI TDFSSDLPTS KAWGWRDIVR
460 470 480 490 500
GIRKVAAPVL STLFPMAAPL IGAADQFIGD LTKTNAAGGR YLTHAAGGRY
510 520 530 540 550
TDVMDSWASG TDTGRFSRNL KDRLESNNYE EMELPPPTKG VIIPVVHTVE
560 570 580 590 600
SAPGEAFGSL LVIIPGAYPE LLDPNQQVLS HFKNDTGCVW GIGEDIPFEG
610 620 630 640 650
DDICYTALPL KEIKKNGNIV VEKVFAGPAM GPSCQLGLSL LVNDIDKGVP
660 670 680 690 700
RMVFTGEIAN DEETIVPICG VDIKAIAAHE HGLPLVGCQP GVDEVVANTS
710 720 730 740 750
LASHLIQSGA LPVQKAQGAS RRIKYLGELM RTTASGMDEE LQKLLHATMA
760 770 780 790 800
RAKEVKDAEV FKLLKLMSWT RKNGLTDHMY EWSKEDPEAV KFGKLISTPP
810 820 830 840 850
KHQEKPKGPD QHTAQEAKAV RISLDAVKAG ADFASPDWIA ENGYRGPSPG
860 870 880 890 900
QFKYYVITGR VPDPRDEYED YVRKPITRPT DMDKIRRLAN SVYGLPHQEP
910 920 930 940 950
APEEFYQAVV EIFAENGGRG PDQDQMQDLR DLARQMKRRP RPAETRRQNR
960 970
APPRAAPSGS SRFTPSGDNG EV
Length:972
Mass (Da):106,768
Last modified:May 1, 1997 - v1
Checksum:i4F9149F65966F226
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB006783 Genomic RNA. Translation: BAA22055.1.
RefSeqiNP_690805.1. NC_004168.1.

Genome annotation databases

GeneIDi995355.
KEGGivg:995355.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB006783 Genomic RNA. Translation: BAA22055.1.
RefSeqiNP_690805.1. NC_004168.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IZJX-ray2.50A/B/C/D/E508-716[»]
4IZKX-ray2.30A/B508-716[»]
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiS50.001.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi995355.
KEGGivg:995355.

Family and domain databases

Gene3Di2.60.120.20. 2 hits.
InterProiIPR002662. Birna_VP2.
IPR002663. Birna_VP3.
IPR025775. Birna_VP4_Prtase_dom.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF01766. Birna_VP2. 1 hit.
PF01767. Birna_VP3. 1 hit.
PF01768. Birna_VP4. 1 hit.
[Graphical view]
PROSITEiPS51548. BIRNAVIRUS_VP4_PRO. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The complete nucleotide sequence of the polyprotein and VP5 gene of a marine birnavirus."
    Suzuki S., Kimura M., Kusuda R.
    Fish. Sci. 64:428-433(1998)
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: Y-6Imported.
  2. "Crystal structures of yellowtail ascites virus VP4 protease: trapping an internal cleavage site trans acyl-enzyme complex in a native Ser/Lys dyad active site."
    Chung I.Y., Paetzel M.
    J. Biol. Chem. 288:13068-13081(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 508-716, DISULFIDE BONDS.

Entry informationi

Entry nameiP89521_9VIRU
AccessioniPrimary (citable) accession number: P89521
Entry historyi
Integrated into UniProtKB/TrEMBL: May 1, 1997
Last sequence update: May 1, 1997
Last modified: June 8, 2016
This is version 55 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.