P14997 (VP2_POVBA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Minor capsid protein VP2 Alternative name(s): Minor structural protein VP2
Organism	BK polyomavirus (strain AS) (BKPyV) [Complete proteome]
Taxonomic identifier	10631 [NCBI]
Taxonomic lineage	Viruses › dsDNA viruses, no RNA stage › Polyomaviridae › Polyomavirus
Virus host	Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	351 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Isoform VP2 is a structural protein that resides within the core of the capsid surrounded by 72 VP1 pentamers. Participates in host cell receptor binding together with VP1. Following virus endocytosis and trafficking to the endoplasmic reticulum, VP2 and VP3 form oligomers and integrate into the endoplasmic reticulum membrane. Heterooligomer VP2-VP3 may create a viroporin for transporting the viral genome across the endoplasmic reticulum membrane to the cytoplasm. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2 or Vp3 nuclear localization signal (shared C-terminus). Plays a role in virion assembly within the nucleus in particular through a DNA-binding domain located in the C-terminal region. A N-terminal myristoylation suggests a scaffold function for virion assembly By similarity. Isoform VP3: structural protein that resides within the core of the capsid surrounded by 72 VP1 pentamers. Following virus endocytosis and trafficking to the endoplasmic reticulum, VP2 and VP3 form oligomers and integrate into the endoplasmic reticulum membrane. Heterooligomer VP2-VP3 may create a viroporin for transporting the viral genome across the endoplasmic reticulum membrane to the cytoplasm. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2 or Vp3 nuclear localization signal (shared C-terminus). Isoform VP3 plays a role in virion assembly within the nucleus. May participate in host cell lysis when associated with VP4 By similarity. Isoform VP4 is a viroporin inducing perforation of cellular membranes to trigger virus progeny release. Forms pores of 3nm inner diameter. VP4 is expressed about 24 hours after the late structural proteins and is not incorporated into the mature virion By similarity.
Subunit structure	Isoform VP2 forms homooligomers, and heterooligomers with VP3 in the endoplasmic reticulum membrane. Isoform VP2 interacts (via D1 domain) with VP1. Isoform VP3 interacts (via D1 domain) with VP1 By similarity.
Subcellular location	Isoform VP2: Virion. Host nucleus. Host endoplasmic reticulum. Host endoplasmic reticulum membrane By similarity. Isoform VP3: Virion. Host nucleus. Host endoplasmic reticulum. Host endoplasmic reticulum membrane By similarity. Isoform VP4: Host nucleus By similarity.
Sequence similarities	Belongs to the polyomaviruses capsid protein VP2 family.

Ontologies

Keywords
Biological process	Cytolysis Initiation of viral infection Viral penetration into host nucleus
Cellular component	Host endoplasmic reticulum Host membrane Host nucleus Membrane Virion
Coding sequence diversity	Alternative initiation Alternative splicing
Developmental stage	Late protein
Domain	Transmembrane Transmembrane helix
Ligand	DNA-binding
Molecular function	Capsid protein
PTM	Lipoprotein Myristate
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	cytolysis Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	host cell endoplasmic reticulum membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 5 isoforms produced by alternative splicing and alternative initiation. [Align] [Select]

Isoform VP2 (identifier: P14997-1)

Also known as: Minor capsid protein VP2;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: Produced by alternative splicing of the late mRNA.

Isoform VP3 (identifier: P14997-2)

Also known as: Minor capsid protein VP3;

The sequence of this isoform differs from the canonical sequence as follows:
     1-119: Missing.

Note: Produced by alternative initiation at Met-120 of isoform VP2.

Isoform VP4 (identifier: P14997-3)

Also known as: Viroporin VP4;

The sequence of this isoform differs from the canonical sequence as follows:
     1-228: Missing.

Note: Produced by alternative initiation at Met-229 of isoform VP2.

Isoform VP1 (identifier: P14996-1)

The sequence of this isoform can be found in the external entry P14996.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by alternative splicing of the late mRNA.

Isoform Agno (identifier: P14998-1)

The sequence of this isoform can be found in the external entry P14998.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by alternative initiation of the late mRNA.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed; by host By similarity
	Chain	2 – 351	350	Minor capsid protein VP2		PRO_0000039203
Regions
	Transmembrane	289 – 309	21	Helical; Potential
	Region	272 – 307	36	D1 By similarity
	Region	312 – 351	40	DNA-binding By similarity
	Motif	315 – 323	9	Nuclear localization signal By similarity
	Compositional bias	3 – 83	81	Ala-rich
Amino acid modifications
	Lipidation	2	1	N-myristoyl glycine; by host By similarity
Natural variations
	Alternative sequence	1 – 228	228	Missing in isoform VP4.		VSP_036013
	Alternative sequence	1 – 119	119	Missing in isoform VP3.		VSP_018915

Sequences

	Sequence		Length	Mass (Da)
	Isoform VP2 (Minor capsid protein VP2) [UniParc]. Last modified January 23, 2007. Version 3. Checksum: D926105B0D1A4130	FASTA	351	38,303
	10 20 30 40 50 60 MGAALALLGD LVASVSEAAA ATGFSVAEIA AGEAAAAIEV QIASLATVEG ITTTSEAIAA 70 80 90 100 110 120 IGLTPQTYAV IAGAPGAIAG FAALIQTVTG ISSLAQVGYR FFSDWDHKVS TVGLYQQSGM 130 140 150 160 170 180 ALELFNPDEY YDILFPGVNT FVNNIQYLDP RHWGPSLFAT ISQALWHVIR DDIPAITSQE 190 200 210 220 230 240 LQRRTERFFR DSLARFLEET TWTIVNAPIN FYNYIQDYYS NLSPIRPSMV RQVAEREGTH 250 260 270 280 290 300 VNFGHTYSID NADSIEEVTQ RMDLRNKESV HSGEFIEKTI APGGANQRTA PQWMLPLLLG 310 320 330 340 350 LYGTVTPALE AYEDGPNQKK RRVSRGSSQK AKGTRASAKT TNKRRSRSSR S
	Isoform VP3 (Minor capsid protein VP3) [UniParc]. Checksum: 0C5A5047989D099A	FASTA	232	26,648
	10 20 30 40 50 60 MALELFNPDE YYDILFPGVN TFVNNIQYLD PRHWGPSLFA TISQALWHVI RDDIPAITSQ 70 80 90 100 110 120 ELQRRTERFF RDSLARFLEE TTWTIVNAPI NFYNYIQDYY SNLSPIRPSM VRQVAEREGT 130 140 150 160 170 180 HVNFGHTYSI DNADSIEEVT QRMDLRNKES VHSGEFIEKT IAPGGANQRT APQWMLPLLL 190 200 210 220 230 GLYGTVTPAL EAYEDGPNQK KRRVSRGSSQ KAKGTRASAK TTNKRRSRSS RS
	Isoform VP4 (Viroporin VP4) [UniParc]. Checksum: 9F9E6E9E28BF4B82	FASTA	123	13,686
	10 20 30 40 50 60 MVRQVAEREG THVNFGHTYS IDNADSIEEV TQRMDLRNKE SVHSGEFIEK TIAPGGANQR 70 80 90 100 110 120 TAPQWMLPLL LGLYGTVTPA LEAYEDGPNQ KKRRVSRGSS QKAKGTRASA KTTNKRRSRS SRS
	Isoform VP1 [UniParc]. See P14996.		–	–
	Isoform Agno [UniParc]. See P14998.		–	–

References

[1]	"Nucleotide sequence of the human polyomavirus AS virus, an antigenic variant of BK virus." Tavis J.E., Walker D.L., Gardner S.D., Frisque R.J. J. Virol. 63:901-911(1989) [PubMed: 2536111] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry." Neu U., Stehle T., Atwood W.J. Virology 384:389-399(2009) [PubMed: 19157478] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M23122 Genomic DNA. Translation: AAA46880.1. M23122 Genomic DNA. Translation: AAA46881.1.
PIR	VVVPAS. E33278.
3D structure databases
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR001070. Polyoma_coat_VP2. [Graphical view]
Pfam	PF00761. Polyoma_coat2. 1 hit. [Graphical view]
PIRSF	PIRSF003377. Polyoma_coat2. 1 hit.
ProtoNet	Search...

Entry information

Entry name

VP2_POVBA

Accession

Primary (citable) accession number: P14997

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	January 23, 2007
Last modified:	December 14, 2011
This is version 58 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program