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Protein

Genome polyprotein

Gene

ORF1

Organism
Porcine enteric sapovirus (isolate Swine/United States/Cowden/1980) (Sw/SV/Cowden/1980/US)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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 p70 processes the polyprotein: Pro-Pol is first released by autocleavage, then all other proteins are cleaved (By similarity). It is also an RNA-directed RNA polymerase which replicates genomic and antigenomic viral RNA by recognizing specific signals. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).By similarity
Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (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)DescriptionActionsGraphical viewLength
Active sitei1078For protease activityBy similarity1
Active sitei1099For protease activityBy similarity1
Active sitei1163For protease activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi464 – 471ATPPROSITE-ProRule annotation8

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

DNA replication, Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Protein family/group databases

MEROPSiC24.003.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 7 chains:
Alternative name(s):
p35
Alternative name(s):
VPg
p14
Protease-polymerase p70 (EC:2.7.7.48, EC:3.4.22.66)
Short name:
Pro-Pol
Capsid protein
Short name:
CP
Alternative name(s):
VP1
p60
Gene namesi
ORF Names:ORF1
OrganismiPorcine enteric sapovirus (isolate Swine/United States/Cowden/1980) (Sw/SV/Cowden/1980/US)
Taxonomic identifieri523795 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeSapovirus
Virus hostiSus scrofa (Pig) [TaxID: 9823]

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003416371 – 2254Genome polyproteinAdd BLAST2254
ChainiPRO_00003416381 – 56Protein p11Add BLAST56
ChainiPRO_000034163957 – 310Protein p28Add BLAST254
ChainiPRO_0000341640311 – 650NTPaseAdd BLAST340
ChainiPRO_0000341641651 – 934Protein p32Add BLAST284
ChainiPRO_0000341642935 – 1048Viral genome-linked proteinAdd BLAST114
ChainiPRO_00003416431049 – 1712Protease-polymerase p70Add BLAST664
ChainiPRO_00003416441713 – 2254Capsid proteinAdd BLAST542

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei956O-(5'-phospho-RNA)-tyrosineBy similarity1

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. Pro-Pol is first autocatalytically cleaved, then processes the whole polyprotein.
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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei56 – 57Cleavage; by Pro-PolBy similarity2
Sitei310 – 311Cleavage; by Pro-PolBy similarity2
Sitei649 – 650Cleavage; by Pro-PolBy similarity2
Sitei934 – 935Cleavage; by Pro-PolBy similarity2
Sitei1047 – 1048Cleavage; by Pro-PolBy similarity2
Sitei1712 – 1713Cleavage; by Pro-PolBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

Capsid protein homodimerizes, then multimerizes.By similarity

Structurei

Secondary structure

12254
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi953 – 966Combined sources14
Helixi972 – 983Combined sources12
Helixi989 – 1003Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MXDNMR-A948-1006[»]
ProteinModelPortaliQ9QEJ5.
SMRiQ9QEJ5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini438 – 592SF3 helicasePROSITE-ProRule annotationAdd BLAST155
Domaini1063 – 1169Peptidase C24Add BLAST107
Domaini1434 – 1559RdRp catalyticPROSITE-ProRule annotationAdd BLAST126

Domaini

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

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

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 3 hits.
InterProiIPR004005. Calicivirus_coat.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR009003. Peptidase_S1_PA.
IPR033703. Rhv-like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative promoter usage. AlignAdd to basket

Isoform Genome polyprotein (identifier: Q9QEJ5-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MANCRPLPIG QLPNRIFDTP RLTPGWVWAC TSEATFKLEW LQDPVVIRPP
60 70 80 90 100
DVFVAQGVVD DFFRPKRVLQ GDPQLIAQVL LGDANGPLVG PVSMQQLTSL
110 120 130 140 150
LHEVSQALSD HKHPLANRYT RASLQRYADT LSNYIPLVDI LTGPKDLTPR
160 170 180 190 200
DVLEQLAAGR EWECVPDSAL KKVFRDMWQY ICEGCDSVYI KLQDVKRKMP
210 220 230 240 250
HIDTTVLKQF IITLTDTISM ATALDTKTWL AHILGWLKPT CLVMIMQQHV
260 270 280 290 300
NSPQGWAATL TALAELYYGI MPLTETLGSV ASWVTDKFAD MATSTWGKFK
310 320 330 340 350
SWWDSLYTPQ AGNDLIILGG VVGLVYFMVF GDAPTQMFTK KLMRVCGFIT
360 370 380 390 400
STVAAIKAAM WIVDYFKQRE HEHQVRITLA RWAALQEVIK QNRCAGLSEV
410 420 430 440 450
TKLKECCEVL LNEVTELMYK LGASPLAGLI RSTSDVIQTT INELAQLMAY
460 470 480 490 500
DTQRKPPAMV VFGGPPGIGK TRLVEALAKQ LGEVSHFTMT VDHYDTYTGN
510 520 530 540 550
TVAIWDEFDV DSKQAFIEAT IGIVNCAPYP LNCDRPEAKG RVFTSKYVLA
560 570 580 590 600
TTNCPTPVMP DHPRAMAFWR RITFIDVTAP TIEQWLVDNP GRKAPTSLFK
610 620 630 640 650
DDFSHLQCSV RGYTAYDEKG NTLSGKVARA RYVSVNNLLD LIKEKYNSEA
660 670 680 690 700
ADVKHLWFTV PQAIHKQARD IILGWLRFHS YPNTVADNIP LSEVRDPTCF
710 720 730 740 750
GYVVISDVDP PRHVAEHVAH IEVESILRTD IVGLLREGGG GLFRALKVKS
760 770 780 790 800
APRNCIINKV MMQAHHTTLQ VLTSQEPHPP NLPRPRRLVF VESPIDIISA
810 820 830 840 850
LRHHVGFCTI PGIVKLITSG VGLGVENLGN FLQSIAGNVR FPLQSECSLL
860 870 880 890 900
RTPSGDVLFY TSGQAAVWAT PARFPIVTPG EASVGKEVCS ESSWWDILKA
910 920 930 940 950
LFSTLVVAFG PIATLVLTAH NLAYLNTREN TLSEAKGKNK RGRGARRAIA
960 970 980 990 1000
LRDDEYDEWQ DIIRDWRKEM TVQQFLDLKE RALSGASDPD SQRYNAWLEL
1010 1020 1030 1040 1050
RAKRLSAGAY QHAVVDIIGK SGHRREVIRT QVMRAPREPK GDTYDSEGRG
1060 1070 1080 1090 1100
YVVPMTAQEK HTGWAVHIGN GRLVTCTHVA NMCDRVAEVE FKVAETDRDT
1110 1120 1130 1140 1150
CIITAPLGHL PSVALGNGPP AFYTTNFHPI RVLDEGSWDT TTTRVTGWRV
1160 1170 1180 1190 1200
VINNGTTTAP GDCGQPYLNA RRQLVGVHAA TSTCGVKKLV SRVQTKKTAK
1210 1220 1230 1240 1250
ATFPWKGLPV TTMPDAGGLP TGTRYHRSIA WPKLLPEETH APAPYGVNDP
1260 1270 1280 1290 1300
RHPFSQHQMI ANNLQPYINT PVALDQTLLQ RAVKHTKGYL DQIIGTHRSP
1310 1320 1330 1340 1350
NLTYAAAVES MAHDTACGPN LPGRKKDYMT DQGEPIGPLK QMLEEAWDMA
1360 1370 1380 1390 1400
HRGVPRRHEY KLALKDELRP IEKNDQGKKR LLWGCDAGVS MIANAVFKPV
1410 1420 1430 1440 1450
TERLVDTVPM HPVAVGICMD SPQIEQMNQA LTGRVLYCLD YSKWDSTQNP
1460 1470 1480 1490 1500
AVTCASVDIL ASYAEDTPLS SAAIATLCSP AVGRLDDIGL TVTSGLPSGM
1510 1520 1530 1540 1550
PFTSVINSVN HMIYFAMAVL EAYEEFKVPY MGNIFDNETI YTYGDDCVYG
1560 1570 1580 1590 1600
LTPATASIMP VVVKNLTSYG LVPTAADKSQ SIEPTDTPVF LKRTFSQTPF
1610 1620 1630 1640 1650
GLRALLDETS LARQCYWVKA NRTTDLFEPA AVDVDIRKNQ LEVMLAYASQ
1660 1670 1680 1690 1700
HPRSVFDKLA GMAEVTASAE GYQLVNVNWA NAVATYNAWY GGTDGGRAPT
1710 1720 1730 1740 1750
NEDEEPEVFV MEAPAPTRSV ASNPEGTQNS NESRPVQPAG PMPVAAAQAL
1760 1770 1780 1790 1800
EMAVATGQIN DTIPSVVRET FSTYTNVTWT TRQPTGTLLA RMSLGPGLNP
1810 1820 1830 1840 1850
YTLHLSAMWA GWGGSFEIKV IISGSGMYAG KLLCALIPPG VDPSAVDQPG
1860 1870 1880 1890 1900
AFPHALVDAR ITDGVTFTLG DVRAVDYHET GVGGAIASLA LYVYQPLINP
1910 1920 1930 1940 1950
FETAVSAAMV TIETRPGPDF GFTLLKPPNQ AMEVGFDPRS LLPRTARTLR
1960 1970 1980 1990 2000
GNRFGRPITA VVIVGVAQQI NRHFSAEGTT LGWSTAPIGP CVARVNGKHT
2010 2020 2030 2040 2050
DNTGRAVFQL GPLSNGPLYP NIINHYPDVA ASTIFNTGTA VNDNTTGGGG
2060 2070 2080 2090 2100
PMVIFNDVGD VVEDVAYQMR FIASHATSQS PTLIDQINAT SMAVCSFGNS
2110 2120 2130 2140 2150
RADLNQNQLN VGIELTYTCG NTAINGIVTS FMDRQYTFGP QGPNNIMLWV
2160 2170 2180 2190 2200
ESVLGTHTGN NTVYSSQPDT VSAALQGQPF NIPDGYMAVW NVNADSADFQ
2210 2220 2230 2240 2250
IGLRRDGYFV TNGAIGTRMV ISEDTTFSFN GMYTLTTPLI GPSGTSGRSI

HSSR
Note: Produced from the genomic RNA.
Length:2,254
Mass (Da):247,170
Last modified:May 1, 2000 - v1
Checksum:i90CA9F0314FAF739
GO
Isoform Subgenomic capsid protein (identifier: Q9QEJ5-2) [UniParc]FASTAAdd to basket
Also known as: VP1

The sequence of this isoform differs from the canonical sequence as follows:
     1-1710: Missing.

Note: Produced from the subgenomic RNA.
Show »
Length:544
Mass (Da):57,615
Checksum:i15FA9B93FA05D946
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0343781 – 1710Missing in isoform Subgenomic capsid protein. CuratedAdd BLAST1710

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF182760 Genomic RNA. Translation: AAF04560.1.
RefSeqiNP_051035.1. NC_000940.1.

Genome annotation databases

GeneIDi1457802.
KEGGivg:1457802.

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF182760 Genomic RNA. Translation: AAF04560.1.
RefSeqiNP_051035.1. NC_000940.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MXDNMR-A948-1006[»]
ProteinModelPortaliQ9QEJ5.
SMRiQ9QEJ5.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC24.003.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1457802.
KEGGivg:1457802.

Family and domain databases

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 3 hits.
InterProiIPR004005. Calicivirus_coat.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR009003. Peptidase_S1_PA.
IPR033703. Rhv-like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_PESV
AccessioniPrimary (citable) accession number: Q9QEJ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Two differents RNAs lead the expression of the capsid protein. One arises from the cleavage of the polyprotein translated from the genomic RNA and the other from the translation of a subgenomic RNA derived from the (-)RNA template. Capsid protein expressed from the subgenomic mRNA is produced in much larger amounts than the cleaved one (By similarity).By similarity

Keywords - Technical termi

3D-structure

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.