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P13900 (POLG_SVDVU) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 144. 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·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 12 chains:

  1. Protein VP0
    Alternative name(s):
    VP4-VP2
  2. Protein VP4
    Alternative name(s):
    P1A
    Virion protein 4
  3. Protein VP2
    Alternative name(s):
    P1B
    Virion protein 2
  4. Protein VP3
    Alternative name(s):
    P1C
    Virion protein 3
  5. Protein VP1
    Alternative name(s):
    P1D
    Virion protein 1
  6. Protease 2A
    Short name=P2A
    EC=3.4.22.29
    Alternative name(s):
    Protein 2A
  7. Protein 2B
    Short name=P2B
  8. Protein 2C
    Short name=P2C
    EC=3.6.1.15
  9. Protein 3A
    Short name=P3A
  10. Protein 3B
    Short name=P3B
    Alternative name(s):
    VPg
  11. Protease 3C
    Short name=P3C
    EC=3.4.22.28
    Alternative name(s):
    Picornain 3C
  12. RNA-directed RNA polymerase 3D-POL
    Short name=P3D-POL
    EC=2.7.7.48
OrganismSwine vesicular disease virus (strain UKG/27/72) (SVDV) [Complete proteome]
Taxonomic identifier12077 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stagePicornaviralesPicornaviridaeEnterovirusEnterovirus B
Virus hostSus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length2185 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Protein VP1: Forms, together with VP2 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Protein VP1 mainly forms the vertices of the capsid. VP1 interacts with host cell receptor to provide virion attachment to target cell. After binding to its receptor, the capsid undergoes conformational changes. VP1 N-terminus (that contains an amphipathic alpha-helix) is externalized, VP4 is released and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks By similarity.

Protein VP2: Forms, together with VP1 and VP3, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome By similarity.

Protein VP3: Forms, together with VP1 and VP2, an icosahedral capsid (pseudo T=3), 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome By similarity.

Protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. VP4 is released, VP1 N-terminus is externalized, and together, they shape a virion-cell connecting channel and a pore in the host membrane through which RNase-protected transfer of the viral genome takes place. After genome has been released, the channel shrinks By similarity.

Protein VP0: Protein VP0: VP0 precursor is a component of immature procapsids, which gives rise to VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step By similarity.

Protease 2A: cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut off the capped cellular mRNA transcription By similarity.

Protein 2B: Affects membrane integrity and cause an increase in membrane permeability By similarity.

Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities By similarity.

Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport By similarity.

Protease 3C: cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease By similarity.

RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals By similarity.

Catalytic activity

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein.

Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.

NTP + H2O = NDP + phosphate.

Subunit structure

Capsid proteins interact with host CXADR.

Subcellular location

Protein VP2: Virion. Host cytoplasm Potential.

Protein VP3: Virion. Host cytoplasm Potential.

Protein VP1: Virion. Host cytoplasm Potential.

Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Protein 3B: Virion Potential.

Protease 3C: Host cytoplasm Potential.

RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.

Post-translational modification

Specific enzymatic cleavages in vivo by the viral proteases yield a variety of precursors and mature proteins. Polyprotein processing intermediates such as VP0 which is a VP4-VP2 precursor are produced. During virion maturation, non-infectious particles are rendered infectious following cleavage of VP0. This maturation cleavage is followed by a conformational change of the particle By similarity.

VPg is uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity.

Myristoylation of VP4 is required during RNA encapsidation and formation of the mature virus particle By similarity.

Sequence similarities

Belongs to the picornaviruses polyprotein family.

Contains 2 peptidase C3 domains.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Ontologies

Keywords
   Biological processActivation of host autophagy by virus
Host gene expression shutoff by virus
Host translation shutoff by virus
Host-virus interaction
Inhibition of host innate immune response by virus
Inhibition of host RIG-I by virus
Inhibition of host RLR pathway by virus
Ion transport
Pore-mediated penetration of viral genome into host cell
Transport
Viral attachment to host cell
Viral immunoevasion
Viral penetration into host cytoplasm
Viral RNA replication
Virus entry into host cell
   Cellular componentCapsid protein
Host cytoplasm
Host cytoplasmic vesicle
Host membrane
Membrane
Virion
   LigandATP-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
Ion channel
Nucleotidyltransferase
Protease
RNA-directed RNA polymerase
Thiol protease
Transferase
Viral ion channel
   PTMCovalent protein-RNA linkage
Lipoprotein
Myristate
Phosphoprotein
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processRNA-protein covalent cross-linking

Inferred from electronic annotation. Source: UniProtKB-KW

induction by virus of host autophagy

Inferred from electronic annotation. Source: UniProtKB-KW

ion transmembrane transport

Inferred from electronic annotation. Source: GOC

pore formation by virus in membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

pore-mediated entry of viral genome into host cell

Inferred from electronic annotation. Source: UniProtKB-KW

protein oligomerization

Inferred from electronic annotation. Source: UniProtKB-KW

proteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host RIG-I activity

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host translation

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: InterPro

transcription, RNA-templated

Inferred from electronic annotation. Source: GOC

viral genome replication

Inferred from electronic annotation. Source: InterPro

virion attachment to host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componenthost cell cytoplasmic vesicle membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

integral to membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

membrane

Inferred from electronic annotation. Source: UniProtKB-KW

viral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA helicase activity

Inferred from electronic annotation. Source: InterPro

RNA-directed RNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

cysteine-type endopeptidase activity

Inferred from electronic annotation. Source: InterPro

ion channel activity

Inferred from electronic annotation. Source: UniProtKB-KW

structural molecule activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host By similarity
Chain2 – 330329Protein VP0 Potential
PRO_0000311085
Chain2 – 6968Protein VP4 Potential
PRO_0000040157
Chain70 – 330261Protein VP2 Potential
PRO_0000040158
Chain331 – 568238Protein VP3 Potential
PRO_0000040159
Chain569 – 851283Protein VP1 Potential
PRO_0000040160
Chain852 – 1001150Protease 2A Potential
PRO_0000040161
Chain1002 – 110099Protein 2B Potential
PRO_0000040162
Chain1101 – 1429329Protein 2C Potential
PRO_0000040163
Chain1430 – 151889Protein 3A Potential
PRO_0000040164
Chain1519 – 154022Protein 3B Potential
PRO_0000040165
Chain1541 – 1723183Protease 3C Potential
PRO_0000040166
Chain1724 – 2185462RNA-directed RNA polymerase 3D-POL Potential
PRO_0000040167

Regions

Topological domain2 – 14951494Cytoplasmic Potential
Intramembrane1496 – 151116 Potential
Topological domain1512 – 2185674Cytoplasmic Potential
Domain1205 – 1361157SF3 helicase
Domain1950 – 2066117RdRp catalytic
Nucleotide binding1229 – 12368ATP Potential

Sites

Active site8721For protease 2A activity By similarity
Active site8901For protease 2A activity By similarity
Active site9611For protease 2A activity By similarity
Active site15801For protease 3C activity Potential
Active site16111For protease 3C activity Potential
Active site16871For protease 3C activity By similarity
Site69 – 702Cleavage Potential
Site330 – 3312Cleavage; by protease 3C Potential
Site851 – 8522Cleavage; by protease 2A Potential
Site1001 – 10022Cleavage; by protease 3C Potential
Site1100 – 11012Cleavage; by protease 3C Potential
Site1429 – 14302Cleavage; by protease 3C Potential
Site1518 – 15192Cleavage; by protease 3C Potential
Site1540 – 15412Cleavage; by protease 3C Potential
Site1723 – 17242Cleavage; by protease 3C Potential

Amino acid modifications

Modified residue15211O-(5'-phospho-RNA)-tyrosine By similarity
Lipidation21N-myristoyl glycine; by host By similarity

Secondary structure

...................................................................................................................................... 2185
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P13900 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: C9B103052934E1B8

FASTA2,185243,365
        10         20         30         40         50         60 
MGAQVSTQKT GAHETSLSAA GNSVIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI 

        70         80         90        100        110        120 
MVKSMPALNS PSAEECGYSD RVRSITLGNS TITTQECANV VVGYGVWPTY LKDEEATAED 

       130        140        150        160        170        180 
QPTQPDVATC RFYTLESVMW QQSSPGWWWK FPDALSNMGL FGQNMQYHYL GRAGYTIHVQ 

       190        200        210        220        230        240 
CNASKFHQGC LLVVCVPEAE MGCATLANKP DPKSLSKGEI ANMFESQNST GETAVQANVI 

       250        260        270        280        290        300 
NAGMGVGVGN LTIFPHQWIN LRTNNSATIV MPYINSVPMD NMFRHNNFTL MVIPFAPLSY 

       310        320        330        340        350        360 
STGATTYVPI TVTVAPMCAE YNGLRLAGKQ GLPTLSTPGS NQFLTSDDFQ SPSAMPQFDV 

       370        380        390        400        410        420 
TPEMDIPGQV NNLMEIAEVD SVVPVNNTEG KVMSIEAYQI PVQSNPTNGS QVFGFPLTPG 

       430        440        450        460        470        480 
ANSVLNRTLL GEILNYYAHW SGSIKLTFMF CGSAMATGKF LLAYSPPGAG APTTRKEAML 

       490        500        510        520        530        540 
GTHVIWDVGL QSSCVLCIPW ISQTHYRYVV MDEYTAGGYI TCWYQTNIVV PADAQSDCKI 

       550        560        570        580        590        600 
LCFVSACNDF SVRMLKDTPF IKQDNFFQGP PGEVMGRAIA RVADTIGSGP VNSESIPALT 

       610        620        630        640        650        660 
AAETGHTSQV VPSDTMQTRH VKNYHSRSES TVENFLCRSA CVFYTTYKNH DSDGDNFAYW 

       670        680        690        700        710        720 
VINTRQVAQL RRKLEMFTYA RFDLELTFVI TSTQEQPTVR GQDAPVLTHQ IMYVPPGGPV 

       730        740        750        760        770        780 
PTKVNSYSWQ TSTNPSVFWT EGSAPPRMSI PFIGIGNAYS MFYDGWARFD KQGTYGISTL 

       790        800        810        820        830        840 
NNMGTLYMRH VNDGGPGPIV STVRIYFKPK HVKTWVPRPP RLCQYQKAGN VNFEPTGVTE 

       850        860        870        880        890        900 
GRTDITTMKT TGAFGQQSGA VYVGNYRVVN RHLATRADWQ NCVWEDYNRD LLVSTTTAHG 

       910        920        930        940        950        960 
CDTIARCDCT AGVYFCASRN KHYPVTFEGP GLVEVQESEY YPKKYQSHVL LAAGFAEPGD 

       970        980        990       1000       1010       1020 
CGGILRCQHG VIGIVTVGGE GVVGFADVRD LLWLEDDAME QGVRDYVEQL GNCFGSGFTN 

      1030       1040       1050       1060       1070       1080 
QICEQVTLLK ESLIGQDSIL EKSLKALVKI VSALVIVVRN HDDLITVTAT LALIGCTTSP 

      1090       1100       1110       1120       1130       1140 
WRWLKQKVSQ YYGIPMAERQ NSGWLKKFTE MTNACKGMEW IAIKIQKFIE WLKVKILPEV 

      1150       1160       1170       1180       1190       1200 
KEKHEFLNRL KQLPLLESQI ATIEQSAPSQ SDQEQLFSNV QYFAHYCRKY APLYAAEAKR 

      1210       1220       1230       1240       1250       1260 
VFSLEKKMSN YIQFKSKCRI EPVCLLLHGS PGAGKSVATN LIGRSLAEKL NSSVYSLPPD 

      1270       1280       1290       1300       1310       1320 
PDHFDGYKQQ AVVIMDDLCQ NPDGKDVSLF CQMVSSVDFV PPMAALEEKG ILFTSPFVLA 

      1330       1340       1350       1360       1370       1380 
STNAGSVNAP TVSDSRALVR RFHFDMNIEV VSMYSQNGKI NMPMAVKTCD EECCPVNFKK 

      1390       1400       1410       1420       1430       1440 
CCPLVCGKAI QFIDRRTQVR YSLDMLVTEM FREYNHRHSV GATLEALFQG PPVYREIKIS 

      1450       1460       1470       1480       1490       1500 
VAPETPPPPA VADLLKSVDS EAVREYCKEK GWLIPEVDST LQIEKHVNRA FICLQALTTF 

      1510       1520       1530       1540       1550       1560 
VSVAGIIYII YKLFAGFQGA YTGMPNQKPR VPTLRQAKVQ GPAFEFAVAM MKRNASTVKT 

      1570       1580       1590       1600       1610       1620 
EYGEFTMLGI YDRWAVLPRH AKPGPTILMN DQVVGVLDAK ELVDKDGTNL ELTLLKLNRN 

      1630       1640       1650       1660       1670       1680 
EKFRDIRGFL AREEVEVNEA VLAINTSKFP NMYIPVGRVT DYGFLNLGGT PTKRMLMYNF 

      1690       1700       1710       1720       1730       1740 
PTRAGQCGGV LMSTGKVLGI HVGGNGHQGF SAALLRHYFN EEQGEIEFIE SSKDAGFPVI 

      1750       1760       1770       1780       1790       1800 
NTPSKTKLEP SVFHHVFEGN KEPAVLRNGD PRLKANFEEA IFSKYIGNVN THVDEYMMEA 

      1810       1820       1830       1840       1850       1860 
VDHYAGQLAT LDISTEPMKL EDAVYGTEGL EALDLTTSAG YPYVALGIKK RDILSKKTRD 

      1870       1880       1890       1900       1910       1920 
LTKLKECMDK YGLNLPMVTY VKDELRSADK VAKGKSRLIE ASSLNDSVAM RQTFGNLYKT 

      1930       1940       1950       1960       1970       1980 
FHLNPGIVTG SAVGCDPDVF WSKIPVMLDG HLIAFDYSGY DASLSPVWFT CLKLLLEKLG 

      1990       2000       2010       2020       2030       2040 
YTNKETNYID YLCNSHHLYR DKHYFVRGGM PSGCSGTSIF NSMINNIIIR TLMLKVYKGI 

      2050       2060       2070       2080       2090       2100 
DLDQFRMIAY GDDVIASYPW PIDASLLAEA GKDYGLIMTP ADKGECFNEV TWTNVTFLKR 

      2110       2120       2130       2140       2150       2160 
YFRADEQYPF LVHPVMPMKD IHESIRWTKD PKNTQDHVRS LCLLAWHNGE HEYEEFIRKI 

      2170       2180 
RSVRVGRCLS LPAFSTLRRK WLDSF 

« Hide

References

[1]"The complete nucleotide sequence of a pathogenic swine vesicular disease virus."
Seechurn P., Knowles N.J., McCauley J.W.
Virus Res. 16:255-274(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"The coxsackie-adenovirus receptor (CAR) is used by reference strains and clinical isolates representing all six serotypes of coxsackievirus group B and by swine vesicular disease virus."
Martino T.A., Petric M., Weingartl H., Bergelson J.M., Opavsky M.A., Richardson C.D., Modlin J.F., Finberg R.W., Kain K.C., Willis N., Gauntt C.J., Liu P.P.
Virology 271:99-108(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HOST CXADR.
[3]"Crystal structure of Swine vesicular disease virus and implications for host adaptation."
Fry E.E., Knowles N.J., Newman J.W., Wilsden G., Rao Z., King A.M., Stuart D.I.
J. Virol. 77:5475-5486(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 71-851.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X54521 Genomic RNA. Translation: CAA38377.1.
PIRGNNYSV. S11670.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1OOPX-ray3.00A569-851[»]
B70-330[»]
C331-568[»]
D1-69[»]
ProteinModelPortalP13900.
SMRP13900. Positions 2-69, 79-568, 581-1001, 1541-2185.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSC03.020.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D4.10.80.10. 2 hits.
InterProIPR003593. AAA+_ATPase.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR014838. P3A.
IPR000081. Peptidase_C3.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR003138. Pico_P1A.
IPR002527. Pico_P2B.
IPR001676. Picornavirus_capsid.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamPF08727. P3A. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF02226. Pico_P1A. 1 hit.
PF00947. Pico_P2A. 1 hit.
PF01552. Pico_P2B. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 3 hits.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
ProDomPD001306. Peptidase_C3. 1 hit.
PD649346. Pico_P2B. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMSSF50494. SSF50494. 2 hits.
SSF52540. SSF52540. 1 hit.
SSF89043. SSF89043. 1 hit.
PROSITEPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP13900.

Entry information

Entry namePOLG_SVDVU
AccessionPrimary (citable) accession number: P13900
Secondary accession number(s): Q84794 expand/collapse secondary AC list , Q84795, Q84796, Q84797, Q84798, Q84799, Q84800, Q84801, Q84802, Q84803, Q84804
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: February 19, 2014
This is version 144 of the entry and version 3 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