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Protein

Structural polyprotein

Gene
N/A
Organism
Infectious pancreatic necrosis virus (strain Sp) (IPNV)
Status
Reviewed-Annotation score: Annotation score: 5 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 (By similarity).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).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.PROSITE-ProRule 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 (By similarity).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).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).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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi26Divalent metal cation; shared with trimeric partnersBy similarity1
Active sitei633NucleophilePROSITE-ProRule annotation1 Publication1
Active sitei674PROSITE-ProRule annotation1 Publication1

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BRENDAi3.4.21.115. 6986.

Protein family/group databases

MEROPSiS50.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Structural polyprotein
Short name:
PP
Cleaved into the following 7 chains:
Precursor of VP2
Short name:
Pre-VP2
Structural peptide 1
Short name:
p1
Structural peptide 2
Short name:
p2
Structural peptide 3
Short name:
p3
Alternative name(s):
Non-structural protein VP4
Short name:
NS
OrganismiInfectious pancreatic necrosis virus (strain Sp) (IPNV)
Taxonomic identifieri11005 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesBirnaviridaeAquabirnavirus
Virus hostiOncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) [TaxID: 8022]
Salmo [TaxID: 8028]
Proteomesi
  • UP000007213 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi508 – 509AS → QL: Complete loss of pVP2-VP4 cleavage. 1 Publication2
Mutagenesisi547H → S: Strongly reduced VP4-VP3 cleavage. No effect on pVP2-VP4 cleavage. 1 Publication1
Mutagenesisi573D → Q: No effect on polyprotein processing. 1 Publication1
Mutagenesisi585D → I: No effect on polyprotein processing. 1 Publication1
Mutagenesisi595D → L: No effect on polyprotein processing. 1 Publication1
Mutagenesisi601D → S: No effect on polyprotein processing. 1 Publication1
Mutagenesisi633S → A, Q or T: Complete loss of protease activity. 1 Publication1
Mutagenesisi633S → C: Partial loss of protease activity. 1 Publication1
Mutagenesisi644D → I: No effect on polyprotein processing. 1 Publication1
Mutagenesisi660 – 661DD → GS: No effect on polyprotein processing. 1 Publication2
Mutagenesisi672D → N: No effect on polyprotein processing. 1 Publication1
Mutagenesisi674K → A, D, H, Q or R: Complete loss of protease activity. 1 Publication1
Mutagenesisi675A → D: 60% loss of pVP2-VP4 and VP4-VP3 cleavages. 1 Publication1
Mutagenesisi676I → A: No effect on polyprotein processing. 1 Publication1
Mutagenesisi677A → D: 60% loss of pVP2-VP4. Complete loss of VP4-VP3 cleavage. 1 Publication1
Mutagenesisi678A → S: No effect on polyprotein processing. 1 Publication1
Mutagenesisi679H → L: Strongly reduced VP4-VP3 cleavage. No effect on pVP2-VP4 cleavage. 1 Publication1
Mutagenesisi680E → M: No effect on polyprotein processing. 1 Publication1
Mutagenesisi682G → L: No effect on polyprotein processing. 1 Publication1
Mutagenesisi683L → A: 60% loss of pVP2-VP4 and VP4-VP3 cleavages. 1 Publication1
Mutagenesisi684P → Q: No effect on polyprotein processing. 1 Publication1
Mutagenesisi685L → A: 60% loss of pVP2-VP4 and VP4-VP3 cleavages. 1 Publication1
Mutagenesisi686I → A: 20% loss of pVP2-VP4 and VP4-VP3 cleavages. 1 Publication1
Mutagenesisi687G → A: 20% loss of pVP2-VP4 and VP4-VP3 cleavages. 1 Publication1
Mutagenesisi689Q → I: No effect on polyprotein processing. 1 Publication1
Mutagenesisi693D → L: Strongly reduced VP4-VP3 cleavage. No effect on pVP2-VP4 cleavage. 1 Publication1
Mutagenesisi704H → S: No effect on polyprotein processing. 1 Publication1
Mutagenesisi734 – 735AS → LE: Complete loss of VP4-VP3 cleavage. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003925991 – 508Precursor of VP2Add BLAST508
ChainiPRO_00002278731 – 442Capsid protein VP2Add BLAST442
PeptideiPRO_0000227874443 – 486Structural peptide 11 PublicationAdd BLAST44
PeptideiPRO_0000227875487 – 495Structural peptide 21 Publication9
PeptideiPRO_0000227876496 – 508Structural peptide 31 PublicationAdd BLAST13
ChainiPRO_0000227877509 – 734Protease VP4Add BLAST226
ChainiPRO_0000227878735 – 972Capsid protein VP3Add BLAST238

Post-translational modificationi

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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei442 – 443Cleavage; by protease VP42
Sitei486 – 487Cleavage; by protease VP42
Sitei495 – 496Cleavage; by protease VP42
Sitei508 – 509Cleavage; by protease VP42
Sitei715 – 716Cleavage; by protease VP4; subsidiary2
Sitei734 – 735Cleavage; by protease VP42

Proteomic databases

PRIDEiQ703G9.

Interactioni

Subunit structurei

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).By similarity

Structurei

Secondary structure

1972
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 15Combined sources7
Helixi17 – 19Combined sources3
Beta strandi32 – 44Combined sources13
Beta strandi51 – 55Combined sources5
Beta strandi60 – 70Combined sources11
Beta strandi74 – 84Combined sources11
Helixi89 – 91Combined sources3
Beta strandi93 – 107Combined sources15
Beta strandi120 – 128Combined sources9
Helixi130 – 132Combined sources3
Helixi140 – 143Combined sources4
Helixi148 – 150Combined sources3
Beta strandi151 – 156Combined sources6
Turni157 – 159Combined sources3
Beta strandi161 – 164Combined sources4
Beta strandi202 – 208Combined sources7
Beta strandi210 – 212Combined sources3
Beta strandi223 – 232Combined sources10
Beta strandi236 – 248Combined sources13
Beta strandi254 – 263Combined sources10
Beta strandi271 – 280Combined sources10
Turni282 – 286Combined sources5
Beta strandi287 – 292Combined sources6
Helixi298 – 300Combined sources3
Beta strandi305 – 313Combined sources9
Helixi317 – 319Combined sources3
Beta strandi324 – 326Combined sources3
Helixi327 – 329Combined sources3
Beta strandi332 – 338Combined sources7
Turni339 – 342Combined sources4
Turni344 – 346Combined sources3
Beta strandi350 – 357Combined sources8
Beta strandi363 – 376Combined sources14
Helixi378 – 381Combined sources4
Helixi395 – 404Combined sources10
Turni405 – 410Combined sources6
Beta strandi413 – 416Combined sources4
Helixi417 – 422Combined sources6
Helixi425 – 427Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliQ703G9.
SMRiQ703G9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ703G9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini509 – 734Peptidase S50PROSITE-ProRule annotationAdd BLAST226

Sequence similaritiesi

Contains 1 peptidase S50 domain.PROSITE-ProRule 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.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q703G9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNTNKATATY LKSIMLPETG PASIPDDITE RHILKQETSS YNLEVSESGS
60 70 80 90 100
GVLVCFPGAP GSRIGAHYRW NANQTGLEFD QWLETSQDLK KAFNYGRLIS
110 120 130 140 150
RKYDIQSSTL PAGLYALNGT LNAATFEGSL SEVESLTYNS LMSLTTNPQD
160 170 180 190 200
KVNNQLVTKG VTVLNLPTGF DKPYVRLEDE TPQGLQSMNG AKMRCTAAIA
210 220 230 240 250
PRRYEIDLPS QRLPPVPATG TLTTLYEGNA DIVNSTTVTG DINFSLAEQP
260 270 280 290 300
ADETKFDFQL DFMGLDNDVP VVTVVSSVLA TNDNYRGVSA KMTQSIPTEN
310 320 330 340 350
ITKPITRVKL SYKINQQTAI GNVATLGTMG PASVSFSSGN GNVPGVLRPI
360 370 380 390 400
TLVAYEKMTP LSILTVAGVS NYELIPNPEL LKNMVTRYGK YDPEGLNYAK
410 420 430 440 450
MILSHREELD IRTVWRTEEY KERTRVFNEI TDFSSDLPTS KAWGWRDIVR
460 470 480 490 500
GIRKVAAPVL STLFPMAAPL IGMADQFIGD LTKTNAAGGR YHSMAAGGRY
510 520 530 540 550
KDVLESWASG GPDGKFSRAL KNRLESANYE EVELPPPSKG VIVPVVHTVK
560 570 580 590 600
SAPGEAFGSL AIIIPGEYPE LLDANQQVLS HFANDTGSVW GIGEDIPFEG
610 620 630 640 650
DNMCYTALPL KEIKRNGNIV VEKIFAGPIM GPSAQLGLSL LVNDIEDGVP
660 670 680 690 700
RMVFTGEIAD DEETIIPICG VDIKAIAAHE QGLPLIGNQP GVDEEVRNTS
710 720 730 740 750
LAAHLIQTGT LPVQRAKGSN KRIKYLGELM ASNASGMDEE LQRLLNATMA
760 770 780 790 800
RAKEVQDAEI YKLLKLMAWT RKNDLTDHMY EWSKEDPDAL KFGKLISTPP
810 820 830 840 850
KHPEKPKGPD QHHAQEARAT RISLDAVRAG ADFATPEWVA LNNYRGPSPG
860 870 880 890 900
QFKYYLITGR EPEPGDEYED YIKQPIVKPT DMNKIRRLAN SVYGLPHQEP
910 920 930 940 950
APEEFYDAVA AVFAQNGGRG PDQDQMQDLR ELARQMKRRP RNADAPRRTR
960 970
APAEPAPPGR SRFTPSGDNA EV
Length:972
Mass (Da):106,646
Last modified:July 5, 2004 - v1
Checksum:i7B1448E99800E3C9
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti883N → Y in AAR10446 (PubMed:15584407).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti36Q → P in strain: Isolate Mason. 1
Natural varianti46S → P in strain: Isolate Mason. 1
Natural varianti52V → 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. 1
Natural varianti54V → I in strain: Isolate NVI-010. 1
Natural varianti82 – 85WLET → CWRA in strain: Isolate Mason. 4
Natural varianti152V → A in strain: Isolate Mason, Isolate Blake and Isolate Tseng. 1
Natural varianti192K → R in strain: Isolate Mason, Isolate Blake and Isolate Tseng. 1
Natural varianti199I → T in strain: Isolate Sp103 and Isolate Sp122. 1
Natural varianti212R → S in strain: Isolate Mason, Isolate Blake and Isolate Tseng. 1
Natural varianti217P → T in strain: Isolate Sp122, Isolate NVI-001, Isolate NVI-011, Isolate NVI-013, Isolate NVI-015, Isolate NVI-020 and Isolate NVI-023. 1
Natural varianti219T → I in strain: Isolate NVI-010. 1
Natural varianti221T → A in strain: Isolate NVI-001, Isolate NVI-013, Isolate NVI-015, Isolate Sp116 and Isolate NVI-023. 1
Natural varianti222L → P in strain: Isolate NVI-011. 1
Natural varianti234N → S in strain: Isolate Tseng. 1
Natural varianti247A → T in strain: Isolate Sp122, Isolate NVI-001, Isolate NVI-013, Isolate NVI-015 and Isolate NVI-023. 1
Natural varianti249Q → R in strain: Isolate Tseng. 1
Natural varianti252D → N in strain: Isolate Mason, Isolate Tseng, Isolate Blake, Isolate Sp103, Isolate NVI-010 and Isolate NVI-016. 1
Natural varianti252D → 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. 1
Natural varianti255K → R in strain: Isolate Mason, Isolate Blake and Isolate Tseng. 1
Natural varianti262F → L in strain: Isolate Mason. 1
Natural varianti288V → A in strain: Isolate Sp116. 1
Natural varianti319A → E in strain: Isolate NVI-016. 1
Natural varianti323V → A in strain: Isolate NVI-020. 1
Natural varianti323V → F in strain: Isolate NVI-016. 1
Natural varianti432 – 434DFS → EKT in strain: Isolate Mason. 3
Natural varianti455V → I in strain: Isolate Mason. 1
Natural varianti473M → T in strain: Isolate Mason, Isolate Heppel and Isolate Blake. 1
Natural varianti500Y → H in strain: Isolate Heppel, Isolate NVI-010, Isolate NVI-011, Isolate NVI-020, Isolate Sp103 and Isolate Sp116. 1
Natural varianti565P → R in strain: Isolate Mason. 1
Natural varianti570 – 571EL → SF in strain: Isolate Mason. 2
Natural varianti672D → A in strain: Isolate NVI-016. 1
Natural varianti717K → Q in strain: Isolate NVI-016. 1
Natural varianti788D → G in strain: Isolate NVI-011. 1
Natural varianti788D → Y in strain: Isolate NVI-001. 1
Natural varianti802H → R in strain: Isolate NVI-015 and Isolate NVI-016. 1
Natural varianti841L → M in strain: Isolate NVI-016. 1
Natural varianti867E → Q in strain: Isolate Mason and Isolate Blake. 1
Natural varianti875P → S in strain: Isolate NVI-016. 1
Natural varianti882M → T in strain: Isolate Tseng. 1
Natural varianti953 – 954AE → GK in strain: Isolate Mason. 2
Natural varianti959 – 960GR → DV in strain: Isolate Mason. 2
Natural varianti968D → N in strain: Isolate Sp116. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliQ703G9.
SMRiQ703G9.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiS50.001.

Proteomic databases

PRIDEiQ703G9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.4.21.115. 6986.

Miscellaneous databases

EvolutionaryTraceiQ703G9.

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...

Entry informationi

Entry nameiPOLS_IPNVS
AccessioniPrimary (citable) accession number: Q703G9
Secondary accession number(s): P90205
, Q4KTX8, Q69CH7, Q69CI0, Q69CI3, Q6U2N3, Q6U2N5, Q6U2N8, Q6U2P1, Q6U2P5, Q6U2P7, Q6UAY7, Q82733, Q990Q0, Q9YJV0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: July 5, 2004
Last modified: November 30, 2016
This is version 61 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

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.