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Q6XDK8 (POLG_SVM10) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 61. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 7 chains:

  1. Protein p11
  2. Protein p28
  3. NTPase
    EC=3.6.1.15
    Alternative name(s):
    p35
  4. Protein p32
  5. Viral genome-linked protein
    Alternative name(s):
    VPg
    p14
  6. Protease-polymerase p70
    Short name=Pro-Pol
    EC=2.7.7.48
    EC=3.4.22.66
  7. Capsid protein
    Short name=CP
    Alternative name(s):
    VP1
    p60
Gene names
ORF Names:ORF1
OrganismSapporo virus (isolate GII/Human/Thailand/Mc10/2000) (Hu/SaV/Mc10/2000/Thailand)
Taxonomic identifier234601 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeSapovirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length2278 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity 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.

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.

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.

Catalytic activity

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).

Subunit structure

Capsid protein homodimerizes, then multimerizes By similarity.

Subcellular location

Capsid protein: Virion. Host cytoplasm.

Domain

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

Post-translational modification

Specific enzymatic cleavages in vivo yield mature proteins. Pro-Pol is first autocatalytically cleaved, then processes the whole polyprotein. Ref.1

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.

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.

Sequence similarities

Contains 1 peptidase C24 domain.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Alternative products

This entry describes 2 isoforms produced by alternative promoter usage. [Align] [Select]
Isoform Genome polyprotein (identifier: Q6XDK8-1)

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.
Note: Produced from the genomic RNA.
Isoform Subgenomic capsid protein (identifier: Q6XDK8-2)

Also known as: VP1;

The sequence of this isoform differs from the canonical sequence as follows:
     1-1720: Missing.
Note: Produced from the subgenomic RNA.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 22782278Genome polyprotein
PRO_0000342101
Chain1 – 6969Protein p11
PRO_0000342102
Chain70 – 325256Protein p28
PRO_0000342103
Chain326 – 666341NTPase
PRO_0000342104
Chain667 – 940274Protein p32
PRO_0000342105
Chain941 – 1055115Viral genome-linked protein
PRO_0000342106
Chain1056 – 1722667Protease-polymerase p70
PRO_0000342107
Chain1723 – 2278556Capsid protein
PRO_5000090469

Regions

Domain454 – 609156SF3 helicase
Domain1071 – 1177107Peptidase C24
Domain1443 – 1568126RdRp catalytic
Nucleotide binding481 – 4888ATP Potential

Sites

Active site10861For protease activity By similarity
Active site11071For protease activity By similarity
Active site11711For protease activity By similarity
Site69 – 702Cleavage; by Pro-Pol
Site325 – 3262Cleavage; by Pro-Pol
Site666 – 6672Cleavage; by Pro-Pol
Site940 – 9412Cleavage; by Pro-Pol
Site1055 – 10562Cleavage; by Pro-Pol
Site1722 – 17232Cleavage; by Pro-Pol

Amino acid modifications

Modified residue9661O-(5'-phospho-RNA)-tyrosine By similarity

Natural variations

Alternative sequence1 – 17201720Missing in isoform Subgenomic capsid protein.
VSP_034390

Experimental info

Mutagenesis10691H → A: No effect on protease activity in vitro. Ref.2
Mutagenesis10751H → A: No effect on protease activity in vitro. Ref.2
Mutagenesis10861H → A: Complete loss of protease activity in vitro. Ref.2
Mutagenesis11071E → A: Complete loss of protease activity in vitro. Ref.2
Mutagenesis11201H → A: No effect on protease activity in vitro. Ref.2
Mutagenesis11361H → A: No effect on protease activity in vitro. Ref.2
Mutagenesis11431E → A: No effect on protease activity in vitro. Ref.2
Mutagenesis11471E → A: No effect on protease activity in vitro. Ref.2
Mutagenesis11711C → A: Complete loss of protease activity in vitro. Ref.1
Mutagenesis11861H → A: No effect on protease activity in vitro. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform Genome polyprotein [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: DE7386F8EE49AD11

FASTA2,278250,097
        10         20         30         40         50         60 
MASKPFYPIE FNPSVELQVL RSAHLRVGGR EQMFETINDL NDHVRGVVAK LWCKHLHRSL 

        70         80         90        100        110        120 
AAAPTFTEEG LLDSFLSKPP VDINPDTTFR ELFGINPHEQ FPLSIHDLAK LQGELVDAAR 

       130        140        150        160        170        180 
NPGHVLRRHY STDSLTALIN KITKFVPVHA TLQEMQARRA FERERAELFR ELPHADLDVS 

       190        200        210        220        230        240 
RQQKSYFYAM WRQVVKKSKE FFIPLVKCTS WRKKFTEPAE IVRQVLVHFC EGMRSQFSTN 

       250        260        270        280        290        300 
ANYINLSLIA KLRPTVLTMI LQQHKNTYRG WLATVTALVE VYSNLFQDMR DTAVSAVSAI 

       310        320        330        340        350        360 
TLVFETIKDF VVNVIDLVKS TFQSQGPTSC GWAAIIAGAL LILMKLSGCS NTTSYWHRLL 

       370        380        390        400        410        420 
KVCGGVTTIA AAARAVVWVR DIIAEADGKA RLKKYMARTA ALLELAASRD VTGTDELKRL 

       430        440        450        460        470        480 
LDCFTQLIEE GTELIQEFGT SPLAGLTRSY VSELESTANS IRSTILLDTP RKTPVAIILT 

       490        500        510        520        530        540 
GPPGIGKTRL AQHLAAGFGK VSNFSVTLDH HDSYTGNEVA IWDEFDVDTQ GKFVETMIGV 

       550        560        570        580        590        600 
VNTAPYPLNC DRVENKGKVF TSDYIICTSN YPTSVLPDNP RAGAFYRRVT TIDVSSPTIE 

       610        620        630        640        650        660 
DWKKKNPGKK PPPDLYKNDF THLRLSVRPF LGYNPEGDTL DGVRVKPVLT SVDGLSRLME 

       670        680        690        700        710        720 
TKFKEQGNEH RNLWITCPRD LVAPAASGLK AYMAANRALA QVFQEPSSQD IGETCTSRVY 

       730        740        750        760        770        780 
VSCNNPPPTY SGRVVKITAI NPWDASLANS MLSMFETTSH IPASIQREIM YRVWDPLVHL 

       790        800        810        820        830        840 
QTREPNTQML PYINRVVPVS SAFDFIRGLR HHLGLCSVKG MWRAYQGWNS SSSILEFLSK 

       850        860        870        880        890        900 
HMADVAFPHN PECTVFRAPD GDVIFYTFGS YACFVSPARV PFVGEPPKNV HSNITRNMTW 

       910        920        930        940        950        960 
AETLRLLAET ITESLVHFGP FLLMMHNVSY LATRSGREEE AKGKTKHGRG AKHARRGGVS 

       970        980        990       1000       1010       1020 
LSDDEYDEWR DLVRDWRQDM TVGEFVELRE RYALGMDSED VQRYRAWLEL RAMRMGAGAY 

      1030       1040       1050       1060       1070       1080 
QHATIIGRGG VQDTIIRTQP MRAPRAPRNQ GYDEEAPTPI VTFTSGGDHI GYGCHMGNGV 

      1090       1100       1110       1120       1130       1140 
VVTVTHVASA SDQVEGQDFA IRKTEGETTW VNTNLGHLPH YQIGDGAPVY YSARLHPVTT 

      1150       1160       1170       1180       1190       1200 
LAEGTYETPN ITVQGYHLRI INGYPTKRGD CGTPYFDSCR RLVGLHAATS TNGETKLAQR 

      1210       1220       1230       1240       1250       1260 
VTKTSKVENA FAWKGLPVVR GPDCGGMPTG TRYHRSPAWP NPVEGETHAP APFGSGDERY 

      1270       1280       1290       1300       1310       1320 
KFSQVEMLVN GLKPYSEPTP GIPPALLQRA ATHTRTYLET IIGTHRSPNL SFSEACSLLE 

      1330       1340       1350       1360       1370       1380 
KSTSCGPFVA GQKGDYWDED KQCYTGVLAE HLAKAWDAAN RGVAPQNAYK LALKDELRPI 

      1390       1400       1410       1420       1430       1440 
EKNAQGKRRL LWGCDAGATL VATAAFKGVA TRLQAVAPMT PVSVGINMDS YQVEVLNESL 

      1450       1460       1470       1480       1490       1500 
KGGVLYCLDY SKWDSTQHPA VTAASLGILE RLSEATPITT SAVELLSSPA RGHLNDIVFI 

      1510       1520       1530       1540       1550       1560 
TKSGLPSGMP FTSVINSLNH MTYFAAAVLK AYEQHGAPYT GNVFQVETVH TYGDDCLYSV 

      1570       1580       1590       1600       1610       1620 
CPATASIFQT VLANLTSFGL KPTAADKSET IAPTHTPVFL KRTLTCTPRG VRGLLDITSI 

      1630       1640       1650       1660       1670       1680 
KRQFLWIKAN RTVDINSPPA YDRDARGIQL ENALAYASQH GHAVFEEVAE LARHTAKAEG 

      1690       1700       1710       1720       1730       1740 
LVLTNVNYDQ ALATYESWFI GGTGLVQGSP SEETTKLVFE MEGLGQPQPQ GGEKTSPQPV 

      1750       1760       1770       1780       1790       1800 
TPQDTIGPTA ALLLPTQIET PNASAQRLEL AMATGAVTSN VPNCIRECFA SVTTIPWTTR 

      1810       1820       1830       1840       1850       1860 
QAANTFLGAI HLGPRINPYT AHLSAMFAGW GGGFQVRVTI SGSGLFAGRA VTAILPPGVN 

      1870       1880       1890       1900       1910       1920 
PASVQNPGVF PHAFIDARTT EPILINLPDI RPVDFHRVDG DDATASVGLW VAQPLINPFQ 

      1930       1940       1950       1960       1970       1980 
TGPVSTCWLS FETRPGPDFD FCLLKAPEQQ MDNGISPASL LPRRLGRSRG NRMGGRIVGL 

      1990       2000       2010       2020       2030       2040 
VVVAAAEQVN HHFDARSTTL GWSTLPVEPI AGDISWYGDA GNKSIRGLVS AQGKGIIFPN 

      2050       2060       2070       2080       2090       2100 
IVNHWTDVAL SSKTSNTTTI PTDTSTLGNL PGASGPLVTF ADNGDVNESS AQNAILTAAN 

      2110       2120       2130       2140       2150       2160 
QNFTSFSPTF DAAGIWVWMP WATDRPGASD SNIYISPTWV NGNPSHPIHE KCTNMIGTNF 

      2170       2180       2190       2200       2210       2220 
QFGGTGTNNI MLWQEQHFTS WPGAAEVYCS QLESTAEIFQ NNIVNIPMNQ MAVFNVETAG 

      2230       2240       2250       2260       2270 
NSFQIAILPN GYCVTNAPVG THQLLDYETS FKFVGLFPQS TSLQGPHGNS GRAVRFLE 

« Hide

Isoform Subgenomic capsid protein (VP1) [UniParc].

Checksum: 56CFD514ADE23DED
Show »

FASTA55859,560

References

[1]"Proteolytic processing of sapovirus ORF1 polyprotein."
Oka T., Katayama K., Ogawa S., Hansman G.S., Kageyama T., Ushijima H., Miyamura T., Takeda N.
J. Virol. 79:7283-7290(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], PROTEOLYTIC PROCESSING OF POLYPROTEIN, MUTAGENESIS OF CYS-1171.
[2]"Highly conserved configuration of catalytic amino acid residues among calicivirus-encoded proteases."
Oka T., Yamamoto M., Yokoyama M., Ogawa S., Hansman G.S., Katayama K., Miyashita K., Takagi H., Tohya Y., Sato H., Takeda N.
J. Virol. 81:6798-6806(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF HIS-1069; HIS-1075; HIS-1086; GLU-1107; HIS-1120; HIS-1136; GLU-1143; GLU-1147 AND HIS-1186.
[3]"Cleavage activity of the sapovirus 3C-like protease in Escherichia coli."
Oka T., Katayama K., Ogawa S., Hansman G.S., Kageyama T., Miyamura T., Takeda N.
Arch. Virol. 150:2539-2548(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1056-1060.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY237420 mRNA. Translation: AAQ17058.2.
RefSeqYP_022762.1. NC_010624.1. [Q6XDK8-1]

3D structure databases

ProteinModelPortalQ6XDK8.
SMRQ6XDK8. Positions 1209-1703.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSC24.003.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID2943313.

Family and domain databases

Gene3D2.60.120.20. 1 hit.
3.40.50.300. 2 hits.
InterProIPR004005. 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.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
IPR029053. Viral_coat.
[Graphical view]
PfamPF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLG_SVM10
AccessionPrimary (citable) accession number: Q6XDK8
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: July 5, 2004
Last modified: July 9, 2014
This is version 61 of the entry and version 1 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