P05844 (POLS_IPNVJ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Structural polyprotein Short name=PP Cleaved into the following 7 chains: Precursor of VP2 Short name=Pre-VP2 Capsid protein VP2 Structural peptide 1 Short name=p1 Structural peptide 2 Short name=p2 Structural peptide 3 Short name=p3 Protease VP4 EC=3.4.21.- Alternative name(s): Non-structural protein VP4 Short name=NS Capsid protein VP3
Organism	Infectious pancreatic necrosis virus (strain Jasper) (IPNV) [Reference proteome]
Taxonomic identifier	11003 [NCBI]
Taxonomic lineage	Viruses › dsRNA viruses › Birnaviridae › Aquabirnavirus › Infectious pancreatic necrosis virus
Virus host	Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) [TaxID: 8022] Salmo [TaxID: 8028]

Protein attributes

Sequence length	972 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.

Ontologies

Keywords
Cellular component	Host cytoplasm Virion
Ligand	Metal-binding
Molecular function	Capsid protein Hydrolase Protease Serine protease T=13 icosahedral capsid protein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	proteolysis Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	T=13 icosahedral viral capsid Inferred from electronic annotation. Source: UniProtKB-KW host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW serine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 972

972

Structural polyprotein

PRO_0000391632

Chain

1 – 508

508

Precursor of VP2

PRO_0000391633

Chain

1 – 442

442

Capsid protein VP2

PRO_0000036780

Peptide

443 – 486

44

Structural peptide 1 By similarity

PRO_0000227859

Peptide

487 – 495

9

Structural peptide 2 By similarity

PRO_0000227860

Peptide

496 – 508

13

Structural peptide 3 By similarity

PRO_0000227861

Chain

509 – 734

226

Protease VP4

PRO_0000036781

Chain

735 – 972

238

Capsid protein VP3

PRO_0000036782

Regions

Domain

509 – 734

226

Peptidase S50

Sites

Active site

633

1

Nucleophile By similarity

Active site

674

1

By similarity

Metal binding

26

1

Divalent metal cation; shared with trimeric partners

Site

442 – 443

2

Cleavage; by protease VP4 By similarity

Site

486 – 487

2

Cleavage; by protease VP4 By similarity

Site

495 – 496

2

Cleavage; by protease VP4 By similarity

Site

508 – 509

2

Cleavage; by protease VP4 By similarity

Site

734 – 735

2

Cleavage; by protease VP4 By similarity

Secondary structure

1

.

.

.

972

Helix Strand Turn

Details...

Helix

968 – 970

3

Sequences

	Sequence		Length	Mass (Da)
	P05844 [UniParc]. Last modified May 30, 2000. Version 2. Checksum: 5CABCD0414EE122B	FASTA	972	106,666
	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

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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M18049 Genomic RNA. Translation: AAA89179.1.

PIR

GNXSIV. A23599.
T09624.

RefSeq

NP_047196.1. NC_001915.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3ZED	X-ray	2.20	D/E/F	733-972	[»]

ProteinModelPortal

P05844.

SMR

P05844. Positions 514-716.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

956513.

Family and domain databases

InterPro

IPR002662. Birna_VP2.
IPR002663. Birna_VP3.
IPR025775. Birna_VP4_Prtase_dom.
[Graphical view]

Pfam

PF01766. Birna_VP2. 1 hit.
PF01767. Birna_VP3. 1 hit.
PF01768. Birna_VP4. 1 hit.
[Graphical view]

PROSITE

PS51548. BIRNAVIRUS_VP4_PRO. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

POLS_IPNVJ

Accession

Primary (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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program