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Protein

Genome polyprotein

Gene

ORF1

Organism
Vesicular exanthema of swine virus serotype A48 (isolate Swine/United States/A48/1948) (VESV)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity (By similarity).By similarity
Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation (By similarity).By similarity
Protease-polymerase p76 processes the polyprotein: Pro-Pol is first released by autocleavage, then all other proteins are cleaved. Cleaves host translation initiation factor eIF4G1 and eIF4G2 thereby inducing a shutdown of host protein synthesis. This shutdown may not prevent viral mRNA from being translated since viral Vpg replaces the cap. May cleave host polyadenylate-binding protein thereby inhibiting cellular translation. It is also an RNA-directed RNA polymerase which replicates genomic and antigenomic viral RNA by recognizing specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).By similarity

Catalytic activityi

NTP + H2O = NDP + phosphate.
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|-Xaa and the P1' position is occupied by Gly-|-Yaa.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei148 – 1492Cleavage; by Pro-PolBy similarity
Sitei435 – 4362Cleavage; by Pro-PolBy similarity
Sitei791 – 7922Cleavage; by Pro-PolBy similarity
Sitei1070 – 10712Cleavage; by Pro-PolBy similarity
Sitei1183 – 11842Cleavage; by Pro-PolBy similarity
Active sitei1222 – 12221For protease activityBy similarity
Active sitei1243 – 12431For protease activityBy similarity
Active sitei1305 – 13051For protease activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi590 – 5978ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Protein family/group databases

MEROPSiC24.002.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 6 chains:
Alternative name(s):
p39
Alternative name(s):
VPg
p13
Protease-polymerase p76 (EC:2.7.7.48, EC:3.4.22.66)
Short name:
Pro-Pol
Gene namesi
ORF Names:ORF1
OrganismiVesicular exanthema of swine virus serotype A48 (isolate Swine/United States/A48/1948) (VESV)
Taxonomic identifieri85617 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostiSus scrofa (Pig) [TaxID: 9823]
ProteomesiUP000007661 Componenti: Genome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 18811881Genome polyproteinPRO_0000402456Add
BLAST
Chaini1 – 148148Protein p16By similarityPRO_0000402457Add
BLAST
Chaini149 – 435287Protein p32By similarityPRO_0000402458Add
BLAST
Chaini436 – 791356NTPaseBy similarityPRO_0000402459Add
BLAST
Chaini792 – 1070279Protein p30By similarityPRO_0000402460Add
BLAST
Chaini1071 – 1183113Viral genome-linked proteinBy similarityPRO_0000402461Add
BLAST
Chaini1184 – 1881698Protease-polymerase p76By similarityPRO_0000402462Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1093 – 10931O-(5'-phospho-RNA)-tyrosineBy similarity

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. Pro-Pol is first autocatalytically cleaved, then processes the whole polyprotein (By similarity).By similarity
VPg is uridylylated by the polymerase and is covalently attached to the 5'-end of the polyadenylated genomic and subgenomic RNAs. This uridylylated form acts as a nucleotide-peptide primer for the polymerase (By similarity).By similarity

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

Protein p32: homodimer, interacts with NTPase, protein p30 and Pro-Pol. Viral genome-linked protein interacts with capsid protein and Pro-Pol. Protease-polymerase p76: Homooligomers, interacts with Vpg, protein p32 and may interact with capsid protein (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliQ9DUN3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini564 – 720157SF3 helicasePROSITE-ProRule annotationAdd
BLAST
Domaini1207 – 1311105Peptidase C24Add
BLAST
Domaini1593 – 1718126RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Domaini

Protease-polymerase is composed of two domains displaying two different catalytic activity. These activities may act independently (By similarity).By similarity

Sequence similaritiesi

Contains 1 peptidase C24 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.300. 6 hits.
InterProiIPR003593. AAA+_ATPase.
IPR016024. ARM-type_fold.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamiPF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 3 hits.
SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9DUN3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQTLSKISN KENASSGLRP KRFKPHQPIP TWMVRCEPLD HDSRRGRDPV
60 70 80 90 100
RASPQAKRVR TPTPYPRHLK PAASAVVRSG NNPSHLKPAS TDVVRSGPQP
110 120 130 140 150
LCCEAKDGGV VRSCKTYNLK PAHESKAVAF SLPKTDGPTG NEPEFIAEAC
160 170 180 190 200
PSCALYDTCP NCTSKVINDD GSTDGTIPSW DQIETTPAFL SLLSNTDEEM
210 220 230 240 250
SADELTNLAA HLRKAFETGS HPANVDYSKD QLQGLLEMAE AAVPPARRQT
260 270 280 290 300
LPFYQQRLEA RRTWREKIFN QPLEEINKIL TTSKDRFQRC AAWKVILEKA
310 320 330 340 350
VLAKEYGEEA YAYAQQALKN INSFDVNLVL KMAAATFIDH IRMMTVDNPD
360 370 380 390 400
LVSYIPKLIV KLKPLTLKMI IDNHENTKEG WLVTLTSLAE LYGMVEVAID
410 420 430 440 450
FVPTVVGKLF DLLMKTTSKM YSMFKSVVLA TFTSESLDFT NPFWYAIAAI
460 470 480 490 500
LCFLITGAIP HNGKMKIHKN ILSNATGIVA GIKAIQALAA MFSTWSNERL
510 520 530 540 550
VNDLSSRTIA LTELNNPTIT ADIDAVINLQ RLAEVLRDEV KSHTLNPLMQ
560 570 580 590 600
PYNPILRNLM SALDKVISCC TRRKAIATKR TAPVAVILTG PPGCGKTTAA
610 620 630 640 650
FALAKRLSQQ KPSIISLDVD HHDTYTGNEV CIIDEFDSSD KVDYANFVVN
660 670 680 690 700
MVNTNPMVLN CDLIENKGKT FTSKYVIMTS NTETPVKPTS RRAGAFYRRV
710 720 730 740 750
MIVDVTNNAV DKWKSDNPGK AVPKWCFNKD FSHLSLSLRG TEPYSKEYVL
760 770 780 790 800
DPTGRNHQSR RAPPPQQITL EQLAQKMVVQ HTTNTSEFVT QAGDVPVFGF
810 820 830 840 850
VCQNNEIDTV YNLLAAVKAR YGANFNLYKG MVRTAHENSG CGAHVHVISR
860 870 880 890 900
EDNFRGKAFT VNRSRLESVP HLEGDSFRRS LGVVMSDKDV TTMFYYIKGK
910 920 930 940 950
VINDQVSLTE LPANQHVVTV HTVYDMAWAL RRHLKWSGQW QLIKAAYEIM
960 970 980 990 1000
CYPDTAACAL RNWMDSTDFS EEHVVTQFIA PGGTIILESC YGARMWATGQ
1010 1020 1030 1040 1050
RLIRAGGLTE AGGPQGGVRF AGLGARNVPW SEILREFMTL ISHIWSQIKG
1060 1070 1080 1090 1100
ATVVLTALTF YLKRFRPRVE AKGKNKNKGP RKNTGVALTD DEYNDWKQSK
1110 1120 1130 1140 1150
AEKNLDLTVK DFLQLRHRAA MGADNTDAVK FRYWYSKKQK IYHDLENFPI
1160 1170 1180 1190 1200
IGRGGLKREL IRKGPLRPRG NDFYDEPDDW YSEGVIDGVT HKNAIVSVDD
1210 1220 1230 1240 1250
VDGMHKGYAI HIGHGVYISL KHVLTGNARI LSEEPKGITI SGELATFRLN
1260 1270 1280 1290 1300
NILPTAVPVG TNKPIKDPWG NPVSTDWQFK NYNTTSGNIY GACGSSCSLT
1310 1320 1330 1340 1350
RQGDCGLPYV DDHGVVVGLH AGSGGDKCPS RKLIVPYVKV DMRIRDTCTK
1360 1370 1380 1390 1400
ESPTKTHKPT FSYRGLLGKE TGEPRTIMKG TRLHVSPAHV DDYEECTHQP
1410 1420 1430 1440 1450
ASLGAGDPRC PISLTGIMVN NLQPYTEASP GPDTATLNRV SKMLTSHMEG
1460 1470 1480 1490 1500
YVPKVHKTEE DSISAFYMLN HDTLCGPYIG ARKKDHVKDG VLDKNLLDLL
1510 1520 1530 1540 1550
SSKWNRAKLG LALPHEYALG LKDELRPKDK VAVGKRRLIW GCDVGVSTVC
1560 1570 1580 1590 1600
AAAFKRVSES IMANHALGFI QVGINMDGPA VEDLFKRLER PKHDRYCVDY
1610 1620 1630 1640 1650
SKWDSTQPPK VTSQSIDILR HFTDKSPIVD SACATLKSNP IGIFNGVAFK
1660 1670 1680 1690 1700
VAGGLPSGMP LTSIINSLNH CLMVGSAVVK ALEDSGVRVT WNIFDSMDLF
1710 1720 1730 1740 1750
TYGDDGVYIV PPLISSVMPK VFANLRQFGL KPTRTDKSDA EITPIPADEP
1760 1770 1780 1790 1800
VEFLKRTIVR TENGVRALLD RSSIIRQFYY IKAENTENWT VPPKRIDTPS
1810 1820 1830 1840 1850
RGQQLYNACL YASQHGEEFY TSKIVPLIER AVKLEGLHIE VPEFHQAVAA
1860 1870 1880
YNGYFNGTEG QPNQIAHASG GLGLSGEVFE N
Length:1,881
Mass (Da):208,813
Last modified:March 1, 2001 - v1
Checksum:i6E487A72523AFE4F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U76874 Genomic RNA. Translation: AAG13641.1.
RefSeqiNP_066255.1. NC_002551.1.

Genome annotation databases

GeneIDi911834.
KEGGivg:911834.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U76874 Genomic RNA. Translation: AAG13641.1.
RefSeqiNP_066255.1. NC_002551.1.

3D structure databases

ProteinModelPortaliQ9DUN3.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC24.002.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi911834.
KEGGivg:911834.

Family and domain databases

Gene3Di3.40.50.300. 6 hits.
InterProiIPR003593. AAA+_ATPase.
IPR016024. ARM-type_fold.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamiPF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 3 hits.
SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The capsid protein of vesicular exanthema of swine virus serotype A48: relationship to the capsid protein of other animal caliciviruses."
    Neill J.D., Meyer R.F., Seal B.S.
    Virus Res. 54:39-50(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Complete nucleotide sequence of the genomic RNA of vesicular exanthema of swine virus A48."
    Neill J.D., Seal B.S., Ridpath J.F.
    Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiPOLG_VESVA
AccessioniPrimary (citable) accession number: Q9DUN3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 30, 2010
Last sequence update: March 1, 2001
Last modified: June 24, 2015
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.