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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)DescriptionActionsGraphical viewLength
Active sitei1012For protease activityBy similarity1
Active sitei1033For protease activityBy similarity1
Active sitei1097For protease activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi408 – 415ATPPROSITE-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 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)DescriptionActionsGraphical viewLength
ChainiPRO_0000341624‹1 – 2208Genome polyproteinAdd BLAST›2208
ChainiPRO_00000369211 – 252Protein p28By similarityAdd BLAST252
ChainiPRO_0000036922253 – 593NTPaseBy similarityAdd BLAST341
ChainiPRO_0000036923594 – 867Protein p32By similarityAdd BLAST274
ChainiPRO_0000036924868 – 981Viral genome-linked proteinBy similarityAdd BLAST114
ChainiPRO_0000036926982 – 1649Protease-polymerase p70By similarityAdd BLAST668
ChainiPRO_00000369271650 – 2208Capsid proteinBy similarityAdd BLAST559

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei893O-(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
Sitei252 – 253Cleavage; by Pro-PolBy similarity2
Sitei593 – 594Cleavage; by Pro-PolBy similarity2
Sitei867 – 868Cleavage; by Pro-PolBy similarity2
Sitei981 – 982Cleavage; by Pro-PolBy similarity2
Sitei1649 – 1650Cleavage; by Pro-PolBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

Capsid protein homodimerizes, then multimerizes.By similarity

Structurei

Secondary structure

12208
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1137 – 1139Combined sources3
Beta strandi1142 – 1146Combined sources5
Beta strandi1157 – 1162Combined sources6
Beta strandi1175 – 1177Combined sources3
Helixi1181 – 1183Combined sources3
Turni1185 – 1187Combined sources3
Helixi1191 – 1199Combined sources9
Helixi1200 – 1203Combined sources4
Helixi1211 – 1229Combined sources19
Helixi1239 – 1245Combined sources7
Beta strandi1248 – 1251Combined sources4
Beta strandi1254 – 1256Combined sources3
Helixi1260 – 1263Combined sources4
Turni1266 – 1268Combined sources3
Helixi1273 – 1287Combined sources15
Beta strandi1295 – 1300Combined sources6
Beta strandi1303 – 1306Combined sources4
Helixi1307 – 1311Combined sources5
Beta strandi1317 – 1321Combined sources5
Helixi1323 – 1341Combined sources19
Turni1342 – 1345Combined sources4
Beta strandi1346 – 1349Combined sources4
Helixi1358 – 1365Combined sources8
Turni1366 – 1369Combined sources4
Beta strandi1370 – 1373Combined sources4
Turni1378 – 1380Combined sources3
Helixi1381 – 1383Combined sources3
Helixi1386 – 1397Combined sources12
Helixi1405 – 1414Combined sources10
Beta strandi1418 – 1421Combined sources4
Beta strandi1424 – 1427Combined sources4
Beta strandi1429 – 1431Combined sources3
Helixi1439 – 1461Combined sources23
Helixi1470 – 1473Combined sources4
Beta strandi1474 – 1479Combined sources6
Beta strandi1482 – 1487Combined sources6
Helixi1489 – 1493Combined sources5
Helixi1495 – 1504Combined sources10
Beta strandi1511 – 1513Combined sources3
Beta strandi1521 – 1523Combined sources3
Beta strandi1529 – 1534Combined sources6
Beta strandi1537 – 1542Combined sources6
Helixi1544 – 1552Combined sources9
Beta strandi1553 – 1560Combined sources8
Helixi1570 – 1585Combined sources16
Helixi1589 – 1606Combined sources18
Helixi1615 – 1628Combined sources14

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ69014.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini382 – 536SF3 helicasePROSITE-ProRule annotationAdd BLAST155
Domaini997 – 1103Peptidase C24Add BLAST107
Domaini1370 – 1495RdRp 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. 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.
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.
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)DescriptionActionsGraphical viewLength
Non-terminal residuei11

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0343841 – 1647Missing in isoform Subgenomic capsid protein. CuratedAdd BLAST1647

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CKWX-ray2.30A1135-1649[»]
2UUTX-ray2.40A1135-1649[»]
2UUWX-ray2.76A1135-1649[»]
2WK4X-ray2.98A/B1135-1649[»]
ProteinModelPortaliQ69014.
SMRiQ69014.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC24.003.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiQ69014.

Family and domain databases

CDDicd00205. rhv_like. 1 hit.
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.
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.
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...

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: November 30, 2016
This is version 113 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.