Q6XDK8 (POLG_SVM10) Reviewed, UniProtKB/Swiss-Prot
Last modified May 1, 2013. Version 52. History...
Names and origin
|Protein names||Recommended name:|
|Organism||Sapporo virus (isolate GII/Human/Thailand/Mc10/2000) (Hu/SaV/Mc10/2000/Thailand)|
|Taxonomic identifier||234601 [NCBI]|
|Taxonomic lineage||Viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Sapovirus ›|
|Virus host||Homo sapiens (Human) [TaxID: 9606]|
|Sequence length||2278 AA.|
|Sequence processing||The displayed sequence is further processed into a mature form.|
|Protein existence||Evidence at protein level|
General annotation (Comments)
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 a 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.
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).
Capsid protein homodimerizes, then multimerizes By similarity.
Protease-polymerase is composed of two domains displaying two different catalytic activity. These activities may act independently.
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.
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.
Contains 1 peptidase C24 domain.
Contains 1 RdRp catalytic domain.
Contains 1 SF3 helicase domain.
|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:
|Note: Produced from the subgenomic RNA.|
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Chain||1 – 2278||2278||Genome polyprotein||PRO_0000342101|
|Chain||1 – 69||69||Protein p11||PRO_0000342102|
|Chain||70 – 325||256||Protein p28||PRO_0000342103|
|Chain||326 – 666||341||NTPase||PRO_0000342104|
|Chain||667 – 940||274||Protein p32||PRO_0000342105|
|Chain||941 – 1055||115||Viral genome-linked protein||PRO_0000342106|
|Chain||1056 – 1722||667||Protease-polymerase p70||PRO_0000342107|
|Chain||1723 – 2278||556||Capsid protein||PRO_5000090469|
|Domain||454 – 609||156||SF3 helicase|
|Domain||1071 – 1177||107||Peptidase C24|
|Domain||1443 – 1568||126||RdRp catalytic|
|Nucleotide binding||481 – 488||8||ATP Potential|
|Active site||1086||1||For protease activity By similarity|
|Active site||1107||1||For protease activity By similarity|
|Active site||1171||1||For protease activity By similarity|
|Site||69 – 70||2||Cleavage; by Pro-Pol|
|Site||325 – 326||2||Cleavage; by Pro-Pol|
|Site||666 – 667||2||Cleavage; by Pro-Pol|
|Site||940 – 941||2||Cleavage; by Pro-Pol|
|Site||1055 – 1056||2||Cleavage; by Pro-Pol|
|Site||1722 – 1723||2||Cleavage; by Pro-Pol|
Amino acid modifications
|Modified residue||966||1||O-(5'-phospho-RNA)-tyrosine By similarity|
|Alternative sequence||1 – 1720||1720||Missing in isoform Subgenomic capsid protein.||VSP_034390|
|Mutagenesis||1069||1||H → A: No effect on protease activity in vitro. Ref.2|
|Mutagenesis||1075||1||H → A: No effect on protease activity in vitro. Ref.2|
|Mutagenesis||1086||1||H → A: Complete loss of protease activity in vitro. Ref.2|
|Mutagenesis||1107||1||E → A: Complete loss of protease activity in vitro. Ref.2|
|Mutagenesis||1120||1||H → A: No effect on protease activity in vitro. Ref.2|
|Mutagenesis||1136||1||H → A: No effect on protease activity in vitro. Ref.2|
|Mutagenesis||1143||1||E → A: No effect on protease activity in vitro. Ref.2|
|Mutagenesis||1147||1||E → A: No effect on protease activity in vitro. Ref.2|
|Mutagenesis||1171||1||C → A: Complete loss of protease activity in vitro. Ref.1|
|Mutagenesis||1186||1||H → A: No effect on protease activity in vitro. Ref.2|
|||"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.
|||"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.
|||"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.
|AY237420 mRNA. Translation: AAQ17058.2.|
|RefSeq||YP_022762.1. NC_010624.1. |
3D structure databases
|HSSP||HSSP built from PDB template 1KHV based on UniProtKB P27410. |
|SMR||Q6XDK8. Positions 1209-1703. |
Protein family/group databases
Protocols and materials databases
Genome annotation databases
Family and domain databases
|InterPro||IPR004005. Calicivirus_coat. |
|Pfam||PF00915. Calici_coat. 1 hit. |
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
|PRINTS||PR00916. 2CENDOPTASE. |
|SUPFAM||SSF50494. Pept_Ser_Cys. 1 hit. |
|PROSITE||PS50507. RDRP_SSRNA_POS. 1 hit. |
PS51218. SF3_HELICASE_2. 1 hit.
|Accession||Primary (citable) accession number: Q6XDK8|
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Viral Protein Annotation Program|