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Protein

Genome polyprotein

Gene

ORF1

Organism
Sapporo virus (strain Human/United Kingdom/Manchester/1993) (Hu/SV/Man/1993/UK)
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 processes the polyprotein: Pro-Pol is first released by autocleavage, then all other proteins are cleaved.By similarity
Protease-polymerase is 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei1012 – 10121For protease activityBy similarity
Active sitei1033 – 10331For protease activityBy similarity
Active sitei1097 – 10971For protease activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi408 – 4158ATPPROSITE-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

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 6 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
OrganismiSapporo virus (strain Human/United Kingdom/Manchester/1993) (Hu/SV/Man/1993/UK)
Taxonomic identifieri82659 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeSapovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini‹1 – 2208›2208Genome polyproteinPRO_0000341624Add
BLAST
Chaini1 – 252252Protein p28By similarityPRO_0000036921Add
BLAST
Chaini253 – 593341NTPaseBy similarityPRO_0000036922Add
BLAST
Chaini594 – 867274Protein p32By similarityPRO_0000036923Add
BLAST
Chaini868 – 981114Viral genome-linked proteinBy similarityPRO_0000036924Add
BLAST
Chaini982 – 1649668Protease-polymerase p70By similarityPRO_0000036926Add
BLAST
Chaini1650 – 2208559Capsid proteinBy similarityPRO_0000036927Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei893 – 8931O-(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.
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)LengthDescriptionGraphical viewFeature identifierActions
Sitei252 – 2532Cleavage; by Pro-PolBy similarity
Sitei593 – 5942Cleavage; by Pro-PolBy similarity
Sitei867 – 8682Cleavage; by Pro-PolBy similarity
Sitei981 – 9822Cleavage; by Pro-PolBy similarity
Sitei1649 – 16502Cleavage; by Pro-PolBy similarity

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

Capsid protein homodimerizes, then multimerizes.By similarity

Structurei

Secondary structure

1
2208
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1137 – 11393Combined sources
Beta strandi1142 – 11465Combined sources
Beta strandi1157 – 11626Combined sources
Beta strandi1175 – 11773Combined sources
Helixi1181 – 11833Combined sources
Turni1185 – 11873Combined sources
Helixi1191 – 11999Combined sources
Helixi1200 – 12034Combined sources
Helixi1211 – 122919Combined sources
Helixi1239 – 12457Combined sources
Beta strandi1248 – 12514Combined sources
Beta strandi1254 – 12563Combined sources
Helixi1260 – 12634Combined sources
Turni1266 – 12683Combined sources
Helixi1273 – 128715Combined sources
Beta strandi1295 – 13006Combined sources
Beta strandi1303 – 13064Combined sources
Helixi1307 – 13115Combined sources
Beta strandi1317 – 13215Combined sources
Helixi1323 – 134119Combined sources
Turni1342 – 13454Combined sources
Beta strandi1346 – 13494Combined sources
Helixi1358 – 13658Combined sources
Turni1366 – 13694Combined sources
Beta strandi1370 – 13734Combined sources
Turni1378 – 13803Combined sources
Helixi1381 – 13833Combined sources
Helixi1386 – 139712Combined sources
Helixi1405 – 141410Combined sources
Beta strandi1418 – 14214Combined sources
Beta strandi1424 – 14274Combined sources
Beta strandi1429 – 14313Combined sources
Helixi1439 – 146123Combined sources
Helixi1470 – 14734Combined sources
Beta strandi1474 – 14796Combined sources
Beta strandi1482 – 14876Combined sources
Helixi1489 – 14935Combined sources
Helixi1495 – 150410Combined sources
Beta strandi1511 – 15133Combined sources
Beta strandi1521 – 15233Combined sources
Beta strandi1529 – 15346Combined sources
Beta strandi1537 – 15426Combined sources
Helixi1544 – 15529Combined sources
Beta strandi1553 – 15608Combined sources
Helixi1570 – 158516Combined sources
Helixi1589 – 160618Combined sources
Helixi1615 – 162814Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CKWX-ray2.30A1135-1649[»]
2UUTX-ray2.40A1135-1649[»]
2UUWX-ray2.76A1135-1649[»]
2WK4X-ray2.98A/B1135-1649[»]
ProteinModelPortaliQ69014.
SMRiQ69014. Positions 1135-1633.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ69014.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini382 – 536155SF3 helicasePROSITE-ProRule annotationAdd
BLAST
Domaini997 – 1103107Peptidase C24Add
BLAST
Domaini1370 – 1495126RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

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

Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR001665. Norovirus_pept_C37.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR009003. Peptidase_S1_PA.
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.
PF05416. Peptidase_C37. 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 (3)i

Sequence statusi: Fragment.

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

This entry describes 3 isoformsi produced by alternative promoter usage and alternative initiation. AlignAdd to basket

Isoform Genome polyprotein (identifier: Q69014-1) [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
MFGTKAPDSV QEGTLFRELF GVDQTEQFPL SLADLARLQG ELVDATRTPG
60 70 80 90 100
HALRQKYTMT TIQDLINKIT KVVPVQATLN EMHARRQFER ERADLFHELP
110 120 130 140 150
LVDEDAVAQP KTYFYTMWRQ VVKKGKAYFC PLVKTSAWRT KISAITEPIK
160 170 180 190 200
DFLIAFWQAV QQEMGVNPQY LQLAWLQKLK PTTLTIILQQ HKHTVSGWLA
210 220 230 240 250
TMTALVEVYS NLFDDLRKSS VTIVSSIGAF FDICKDFVSQ VVELVKTTFT
260 270 280 290 300
AQGPTDLGWA AVLAGAAMIL LKMSGCPGVI GMWTKVLKIC GGITTITAAA
310 320 330 340 350
RGVRWLKDLY EEAEGRRLPK MYMARGAALI ELAASREVTG VDELKGLLDC
360 370 380 390 400
FTILIEEGTE LIHKFGTSPL AGLVRTYVSE LETQANNIRS TIKLDTPRRV
410 420 430 440 450
PVVIILTGAP GIGKTRLAQY IGQRFGKTSN FSVAVDHHDG YTGNTVCIWD
460 470 480 490 500
EFDVDSKGAF VETMIGIANT APFPLNCDRV ENKGRVFTSD YVICTSNYPT
510 520 530 540 550
SVIPDNPRAA AFYRRVLTVD VSAPDLEEWK KRNPGKRPTP DLYQDDFSHL
560 570 580 590 600
KLMLRPYLGY NPDGDTLEGP RVAPTQISIA GLITLMERRF KEQAGPLQNL
610 620 630 640 650
WLQVPKTLVE QSTNMVKAFM YANRAVCDVI PNPATRDITE TALSKVFVCG
660 670 680 690 700
TAPPPEFVGK HIVITGIEVG DASIANSLLS MFTTTTRLSA AAQREYMYRV
710 720 730 740 750
WSPLIHIQDR SMNTQNLPYI NRVIPVTSHW DFLRGLRHHL GFTSIPGMWK
760 770 780 790 800
AFQGWRTSQG IVDFVAHHMA DVTFPSNPEC TIFRTPDADV VFYTFGSYVC
810 820 830 840 850
FATPARVPYV GTPPTTIHSN TPRCMTWGET LALLCEVVAE FVLHFGPVIL
860 870 880 890 900
SAANIAYLMT RGSRTEEAKG KTKHGRGMRH GHRAGVSLSD DEYDEWRDLM
910 920 930 940 950
RDWRRDMSVN DFLMLRERSA LGMDDEDVAR YRAWLEIRAM RMAGGAYTHA
960 970 980 990 1000
TIIGRGGVRD EIIRTSPRRA PTRPQQHYEE EGPTAIVEFT QGGDHIGYGV
1010 1020 1030 1040 1050
HIGNGNVITV THVASTSDEV NGSAFKITRT VGETTWVQGP FSQLPHMQIG
1060 1070 1080 1090 1100
SGSPVYFTTR LHPVFTISEG TFETPNITVN GFHVRIMNGY PTKKGDCGLP
1110 1120 1130 1140 1150
YFNSNRQLVA LHAGTDTQGE TKVAQRVVKE VTTQDEFQWK GLPVVKSGLD
1160 1170 1180 1190 1200
VGGMPTGTRY HRSPAWPEEQ PGETHAPAPF GSGDKRYTFS QTEMLVNGLK
1210 1220 1230 1240 1250
PYTEPTAGVP PQLLSRAVTH VRSYIETIIG THRSPVLTYH QACELLERTT
1260 1270 1280 1290 1300
SCGPFVQGLK GDYWDEEQQQ YTGVLANHLE QAWDKANKGI APRNAYKLAL
1310 1320 1330 1340 1350
KDELRPIEKN KAGKRRLLWG CDAATTLIAT AAFKAVATRL QVVTPMTPVA
1360 1370 1380 1390 1400
VGINMDSVQM QVMNDSLKGG VLYCLDYSKW DSTQNPAVTA ASLAILERFA
1410 1420 1430 1440 1450
EPHPIVSCAI EALSSPAEGY VNDIKFVTRG GLPSGMPFTS VVNSINHMIY
1460 1470 1480 1490 1500
VAAAILQAYE SHNVPYTGNV FQVETIHTYG DDCMYSVCPA TASIFHTVLA
1510 1520 1530 1540 1550
NLTSYGLKPT AADKSDAIKP TNTPVFLKRT FTQTPHGIRA LLDITSITRQ
1560 1570 1580 1590 1600
FYWLKANRTS DPSSPPAFDR QARSAQLENA LAYASQHGPV MFDTVRQIAI
1610 1620 1630 1640 1650
KTAQGEGLVL VNTNYDQALA TYNAWFIGGT VPDPVGHTEG THKIVFEMEG
1660 1670 1680 1690 1700
NGSNPEPKQS NNPMVVDPPG TTGPTTSHVV VANPEQPNGA AQRLELAVAT
1710 1720 1730 1740 1750
GAIQSNVPEA IRNCFAVFRT FAWNDRMPTG TFLGSISLHP NINPYTSHLS
1760 1770 1780 1790 1800
GMWAGWGGSF EVRLSISGSG VFAGRIIASV IPPGVDPSSI RDPGVLPHAF
1810 1820 1830 1840 1850
VDARITEPVS FMIPDVRAVD YHRMDGAEPT CSLGFWVYQP LLNPFSTTAV
1860 1870 1880 1890 1900
STCWVSVETK PGGDFDFCLL RPPGQQMENG VSPEGLLPRR LGYSRGNRVG
1910 1920 1930 1940 1950
GLVVGMILVA EHKQVNRHFN SNSVTFGWST APVNPMAAEI VTNQAHSTSR
1960 1970 1980 1990 2000
HAWLSIGAQN KGPLFPGIPN HFPDSCASTV VGAMDTSLGG RPSTGVCGPA
2010 2020 2030 2040 2050
ISFQNNGDVY ENDTPSVMFA TYDPLTSGTG VALTNSINPA SLALVRISNN
2060 2070 2080 2090 2100
DFDTSGFAND KNVVVQMSWE MYTGTNQIRG QVTPMSGTNY TFTSTGANTL
2110 2120 2130 2140 2150
VLWQERMLSY DGHQAILYSS QLERTAEYFQ NDIVNIPENS MAVFNVETNS
2160 2170 2180 2190 2200
ASFQIGIRPD GYMVTGGSIG VNVPLEPETR FQYVGILPLS AALSGPSGNM

GRARRVFQ
Note: Produced from the genomic RNA.
Length:2,208
Mass (Da):242,737
Last modified:November 1, 1997 - v1
Checksum:i3E299D5BA20E45DC
GO
Isoform Subgenomic capsid protein (identifier: Q69014-2) [UniParc]FASTAAdd to basket

Also known as: VP1

The sequence of this isoform differs from the canonical sequence as follows:
     1-1647: Missing.

Note: Produced from the subgenomic RNA.
Show »
Length:561
Mass (Da):60,115
Checksum:iEF915A38359E38FF
GO
Isoform Uncharacterized protein VP3 (identifier: Q69015-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry Q69015.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative initiation from the subgenomic RNA.
Length:161
Mass (Da):17,469
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Non-terminal residuei1 – 11

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 16471647Missing in isoform Subgenomic capsid protein. CuratedVSP_034384Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X86560 Genomic RNA. Translation: CAA60262.1.

Keywords - Coding sequence diversityi

Alternative initiation, Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X86560 Genomic RNA. Translation: CAA60262.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CKWX-ray2.30A1135-1649[»]
2UUTX-ray2.40A1135-1649[»]
2UUWX-ray2.76A1135-1649[»]
2WK4X-ray2.98A/B1135-1649[»]
ProteinModelPortaliQ69014.
SMRiQ69014. Positions 1135-1633.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC24.003.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiQ69014.

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR001665. Norovirus_pept_C37.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR009003. Peptidase_S1_PA.
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.
PF05416. Peptidase_C37. 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...

Publicationsi

  1. "Human enteric caliciviruses have a unique genome structure and are distinct from the Norwalk-like viruses."
    Liu B.L., Clarke I.N., Caul E.O., Lambden P.R.
    Arch. Virol. 140:1345-1356(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Structural and functional characterization of sapovirus RNA-dependent RNA polymerase."
    Fullerton S.W., Blaschke M., Coutard B., Gebhardt J., Gorbalenya A., Canard B., Tucker P.A., Rohayem J.
    J. Virol. 81:1858-1871(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1135-1649.

Entry informationi

Entry nameiPOLG_SVM93
AccessioniPrimary (citable) accession number: Q69014
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: October 14, 2015
This is version 109 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

Caution

The N-terminal part of the polyprotein may be missing and the genome sequence may lack the 5'-end, since all other sapoviruses code for a supplemental N-terminal peptide.Curated

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.