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Q6XDK8

- POLG_SVM10

UniProt

Q6XDK8 - POLG_SVM10

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Protein
Genome polyprotein
Gene
ORF1
Organism
Sapporo virus (isolate GII/Human/Thailand/Mc10/2000) (Hu/SaV/Mc10/2000/Thailand)
Status
Reviewed - 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.
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 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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei69 – 702Cleavage; by Pro-Pol
Sitei325 – 3262Cleavage; by Pro-Pol
Sitei666 – 6672Cleavage; by Pro-Pol
Sitei940 – 9412Cleavage; by Pro-Pol
Sitei1055 – 10562Cleavage; by Pro-Pol
Active sitei1086 – 10861For protease activity By similarity
Active sitei1107 – 11071For protease activity By similarity
Active sitei1171 – 11711For protease activity By similarity
Sitei1722 – 17232Cleavage; by Pro-Pol

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi481 – 4888ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. RNA binding Source: InterPro
  3. RNA helicase activity Source: InterPro
  4. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  5. cysteine-type endopeptidase activity Source: InterPro
Complete GO annotation...

GO - Biological processi

  1. DNA replication Source: UniProtKB-KW
  2. RNA-protein covalent cross-linking Source: UniProtKB-KW
  3. transcription, DNA-templated Source: InterPro
  4. viral RNA genome replication Source: InterPro
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
OrganismiSapporo virus (isolate GII/Human/Thailand/Mc10/2000) (Hu/SaV/Mc10/2000/Thailand)
Taxonomic identifieri234601 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeSapovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]

Subcellular locationi

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-SubCell
  2. viral capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1069 – 10691H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1075 – 10751H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1086 – 10861H → A: Complete loss of protease activity in vitro. 1 Publication
Mutagenesisi1107 – 11071E → A: Complete loss of protease activity in vitro. 1 Publication
Mutagenesisi1120 – 11201H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1136 – 11361H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1143 – 11431E → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1147 – 11471E → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1171 – 11711C → A: Complete loss of protease activity in vitro. 1 Publication
Mutagenesisi1186 – 11861H → A: No effect on protease activity in vitro. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 22782278Genome polyprotein
PRO_0000342101Add
BLAST
Chaini1 – 6969Protein p11
PRO_0000342102Add
BLAST
Chaini70 – 325256Protein p28
PRO_0000342103Add
BLAST
Chaini326 – 666341NTPase
PRO_0000342104Add
BLAST
Chaini667 – 940274Protein p32
PRO_0000342105Add
BLAST
Chaini941 – 1055115Viral genome-linked protein
PRO_0000342106Add
BLAST
Chaini1056 – 1722667Protease-polymerase p70
PRO_0000342107Add
BLAST
Chaini1723 – 2278556Capsid protein
PRO_5000090469Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei966 – 9661O-(5'-phospho-RNA)-tyrosine By similarity

Post-translational modificationi

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

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

Capsid protein homodimerizes, then multimerizes By similarity.

Structurei

3D structure databases

ProteinModelPortaliQ6XDK8.
SMRiQ6XDK8. Positions 1209-1703.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini454 – 609156SF3 helicase
Add
BLAST
Domaini1071 – 1177107Peptidase C24
Add
BLAST
Domaini1443 – 1568126RdRp catalytic
Add
BLAST

Domaini

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

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 2 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.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
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. Align

Isoform Genome polyprotein (identifier: Q6XDK8-1) [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

MASKPFYPIE FNPSVELQVL RSAHLRVGGR EQMFETINDL NDHVRGVVAK     50
LWCKHLHRSL AAAPTFTEEG LLDSFLSKPP VDINPDTTFR ELFGINPHEQ 100
FPLSIHDLAK LQGELVDAAR NPGHVLRRHY STDSLTALIN KITKFVPVHA 150
TLQEMQARRA FERERAELFR ELPHADLDVS RQQKSYFYAM WRQVVKKSKE 200
FFIPLVKCTS WRKKFTEPAE IVRQVLVHFC EGMRSQFSTN ANYINLSLIA 250
KLRPTVLTMI LQQHKNTYRG WLATVTALVE VYSNLFQDMR DTAVSAVSAI 300
TLVFETIKDF VVNVIDLVKS TFQSQGPTSC GWAAIIAGAL LILMKLSGCS 350
NTTSYWHRLL KVCGGVTTIA AAARAVVWVR DIIAEADGKA RLKKYMARTA 400
ALLELAASRD VTGTDELKRL LDCFTQLIEE GTELIQEFGT SPLAGLTRSY 450
VSELESTANS IRSTILLDTP RKTPVAIILT GPPGIGKTRL AQHLAAGFGK 500
VSNFSVTLDH HDSYTGNEVA IWDEFDVDTQ GKFVETMIGV VNTAPYPLNC 550
DRVENKGKVF TSDYIICTSN YPTSVLPDNP RAGAFYRRVT TIDVSSPTIE 600
DWKKKNPGKK PPPDLYKNDF THLRLSVRPF LGYNPEGDTL DGVRVKPVLT 650
SVDGLSRLME TKFKEQGNEH RNLWITCPRD LVAPAASGLK AYMAANRALA 700
QVFQEPSSQD IGETCTSRVY VSCNNPPPTY SGRVVKITAI NPWDASLANS 750
MLSMFETTSH IPASIQREIM YRVWDPLVHL QTREPNTQML PYINRVVPVS 800
SAFDFIRGLR HHLGLCSVKG MWRAYQGWNS SSSILEFLSK HMADVAFPHN 850
PECTVFRAPD GDVIFYTFGS YACFVSPARV PFVGEPPKNV HSNITRNMTW 900
AETLRLLAET ITESLVHFGP FLLMMHNVSY LATRSGREEE AKGKTKHGRG 950
AKHARRGGVS LSDDEYDEWR DLVRDWRQDM TVGEFVELRE RYALGMDSED 1000
VQRYRAWLEL RAMRMGAGAY QHATIIGRGG VQDTIIRTQP MRAPRAPRNQ 1050
GYDEEAPTPI VTFTSGGDHI GYGCHMGNGV VVTVTHVASA SDQVEGQDFA 1100
IRKTEGETTW VNTNLGHLPH YQIGDGAPVY YSARLHPVTT LAEGTYETPN 1150
ITVQGYHLRI INGYPTKRGD CGTPYFDSCR RLVGLHAATS TNGETKLAQR 1200
VTKTSKVENA FAWKGLPVVR GPDCGGMPTG TRYHRSPAWP NPVEGETHAP 1250
APFGSGDERY KFSQVEMLVN GLKPYSEPTP GIPPALLQRA ATHTRTYLET 1300
IIGTHRSPNL SFSEACSLLE KSTSCGPFVA GQKGDYWDED KQCYTGVLAE 1350
HLAKAWDAAN RGVAPQNAYK LALKDELRPI EKNAQGKRRL LWGCDAGATL 1400
VATAAFKGVA TRLQAVAPMT PVSVGINMDS YQVEVLNESL KGGVLYCLDY 1450
SKWDSTQHPA VTAASLGILE RLSEATPITT SAVELLSSPA RGHLNDIVFI 1500
TKSGLPSGMP FTSVINSLNH MTYFAAAVLK AYEQHGAPYT GNVFQVETVH 1550
TYGDDCLYSV CPATASIFQT VLANLTSFGL KPTAADKSET IAPTHTPVFL 1600
KRTLTCTPRG VRGLLDITSI KRQFLWIKAN RTVDINSPPA YDRDARGIQL 1650
ENALAYASQH GHAVFEEVAE LARHTAKAEG LVLTNVNYDQ ALATYESWFI 1700
GGTGLVQGSP SEETTKLVFE MEGLGQPQPQ GGEKTSPQPV TPQDTIGPTA 1750
ALLLPTQIET PNASAQRLEL AMATGAVTSN VPNCIRECFA SVTTIPWTTR 1800
QAANTFLGAI HLGPRINPYT AHLSAMFAGW GGGFQVRVTI SGSGLFAGRA 1850
VTAILPPGVN PASVQNPGVF PHAFIDARTT EPILINLPDI RPVDFHRVDG 1900
DDATASVGLW VAQPLINPFQ TGPVSTCWLS FETRPGPDFD FCLLKAPEQQ 1950
MDNGISPASL LPRRLGRSRG NRMGGRIVGL VVVAAAEQVN HHFDARSTTL 2000
GWSTLPVEPI AGDISWYGDA GNKSIRGLVS AQGKGIIFPN IVNHWTDVAL 2050
SSKTSNTTTI PTDTSTLGNL PGASGPLVTF ADNGDVNESS AQNAILTAAN 2100
QNFTSFSPTF DAAGIWVWMP WATDRPGASD SNIYISPTWV NGNPSHPIHE 2150
KCTNMIGTNF QFGGTGTNNI MLWQEQHFTS WPGAAEVYCS QLESTAEIFQ 2200
NNIVNIPMNQ MAVFNVETAG NSFQIAILPN GYCVTNAPVG THQLLDYETS 2250
FKFVGLFPQS TSLQGPHGNS GRAVRFLE 2278

Note: Produced from the genomic RNA.

Length:2,278
Mass (Da):250,097
Last modified:July 5, 2004 - v1
Checksum:iDE7386F8EE49AD11
GO
Isoform Subgenomic capsid protein (identifier: Q6XDK8-2) [UniParc]FASTAAdd to Basket

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.

Show »
Length:558
Mass (Da):59,560
Checksum:i56CFD514ADE23DED
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 17201720Missing in isoform Subgenomic capsid protein.
VSP_034390Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY237420 mRNA. Translation: AAQ17058.2.
RefSeqiYP_022762.1. NC_010624.1. [Q6XDK8-1]

Genome annotation databases

GeneIDi2943313.

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY237420 mRNA. Translation: AAQ17058.2 .
RefSeqi YP_022762.1. NC_010624.1. [Q6XDK8-1 ]

3D structure databases

ProteinModelPortali Q6XDK8.
SMRi Q6XDK8. Positions 1209-1703.
ModBasei Search...

Protein family/group databases

MEROPSi C24.003.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 2943313.

Family and domain databases

Gene3Di 2.60.120.20. 1 hit.
3.40.50.300. 2 hits.
InterProi IPR004005. 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 ]
Pfami PF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view ]
PRINTSi PR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. 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.

Entry informationi

Entry nameiPOLG_SVM10
AccessioniPrimary (citable) accession number: Q6XDK8
Entry historyi
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 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.

Keywords - Technical termi

Direct protein sequencing

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