Q672I1 (POLG_SVSAP) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 7 chains: Protein p11 Protein p28 NTPase EC=3.6.1.15 Alternative name(s): p35 Protein p32 Viral genome-linked protein Alternative name(s): VPg p14 Protease-polymerase p70 Short name=Pro-Pol EC=2.7.7.48 EC=3.4.22.66 Capsid protein Short name=CP Alternative name(s): VP1 p60
Organism	Sapporo virus (isolate GI/Human/Germany/pJG-Sap01) (Hu/Dresden/pJG-Sap01/DE) [Reference proteome]
Taxonomic identifier	291175 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Sapovirus › Sapporo virus › Sapovirus unknown genotype
Virus host	Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	2280 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

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 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.
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. 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.

Ontologies

Keywords
Biological process	DNA replication Viral RNA replication
Cellular component	Host cytoplasm Virion
Coding sequence diversity	Alternative initiation Alternative promoter usage
Ligand	ATP-binding Nucleotide-binding
Molecular function	Capsid protein Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
PTM	Covalent protein-RNA linkage Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative promoter usage. [Align] [Select]

Isoform Genome polyprotein (identifier: Q672I1-1)

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: Q672I1-2)

Also known as: VP1;

The sequence of this isoform differs from the canonical sequence as follows:
     1-1719: Missing.

Note: Produced from the subgenomic RNA.

Isoform Uncharacterized protein VP3 (identifier: Q672I0-1)

The sequence of this isoform can be found in the external entry Q672I0.
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.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 2280	2280	Genome polyprotein		PRO_0000342108
	Chain	1 – 68	68	Protein p11		PRO_0000342109
	Chain	69 – 324	256	Protein p28		PRO_0000342110
	Chain	325 – 665	341	NTPase		PRO_0000342111
	Chain	666 – 939	274	Protein p32		PRO_0000342112
	Chain	940 – 1053	114	Viral genome-linked protein		PRO_0000342113
	Chain	1054 – 1721	668	Protease-polymerase p70		PRO_0000342114
	Chain	1722 – 2280	559	Capsid protein		PRO_0000342115
Regions
	Domain	454 – 608	155	SF3 helicase
	Domain	1069 – 1175	107	Peptidase C24
	Domain	1442 – 1567	126	RdRp catalytic
	Nucleotide binding	480 – 487	8	ATP Potential
Sites
	Active site	1084	1	For protease activity By similarity
	Active site	1105	1	For protease activity By similarity
	Active site	1169	1	For protease activity By similarity
	Site	68 – 69	2	Cleavage; by Pro-Pol By similarity
	Site	324 – 325	2	Cleavage; by Pro-Pol By similarity
	Site	665 – 666	2	Cleavage; by Pro-Pol By similarity
	Site	939 – 940	2	Cleavage; by Pro-Pol By similarity
	Site	1053 – 1054	2	Cleavage; by Pro-Pol By similarity
	Site	1721 – 1722	2	Cleavage; by Pro-Pol By similarity
Amino acid modifications
	Modified residue	965	1	O-(5'-phospho-RNA)-tyrosine By similarity
Natural variations
	Alternative sequence	1 – 1719	1719	Missing in isoform Subgenomic capsid protein.		VSP_034391

Sequences

	Sequence		Length	Mass (Da)
	Isoform Genome polyprotein [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 2402A87ACE40873F	FASTA	2,280	251,007
	10 20 30 40 50 60 MVSKPFKPIV LNATFEWQVF KRCYLRVAPR EAFCENLSEL HHYFARRVNA WLKHATRTLP 70 80 90 100 110 120 DGYTFVEEGL LDMFGTKAPD SVQEGTLFRE LFGVDQTEQF PLSLADLAKL QGELVDATRT 130 140 150 160 170 180 PGHALRQKYT MTTIQDLINK ITKVVPVQAT LTEMHARRQF ERERADLFHE LPLVDEDAVS 190 200 210 220 230 240 QPKTYFYTMW RQVVKKGKAY FCPLVKTSAW RTKISAITEP IKDFLIAFCQ AVQQEMGVNP 250 260 270 280 290 300 QYLQLAWLQK LKPTTLTIIL QQHKYTVSGW LATMTALVEV YSNLFDDLRK SSVAIVSSIG 310 320 330 340 350 360 AFFDICKDFV SQVVELVKTT FTAQGPTDLG WAAVLAGAAM ILLKMSGCPG VIGMWTKVLK 370 380 390 400 410 420 ICGGITTITA AARGVRWLKD LYEEAEGRRL AKMYMARGAA LIELAASREV TGIDELKGLL 430 440 450 460 470 480 DCFTILIEEG TELIHKFGTS PLAGLVRTYV SELETQANNI RSTIKLDTPR RVPVVIILTG 490 500 510 520 530 540 APGIGKTRLA QYVGQRFGKT SNFSVAVDHH DGYTGNTVCI WDEFDVDSKG AFVETMIGIA 550 560 570 580 590 600 NTAPFPLNCD RVENKGRVFT SDYVICTSNY PTSVIPDNPR AAAFYRRVLT VDVSAPDLEE 610 620 630 640 650 660 WKKRNPGKRP TPDLYQDDFS HLKLMLRPYL GYNPDGDTLE GPRVAPTQIS IAGLITLMER 670 680 690 700 710 720 RFKEQAGPLQ NLWLQVPKTL VEQSTNMVKA FMYANRAVCD VIPNPATRDI AETALTKIFV 730 740 750 760 770 780 CGTAPPPEFV GKHIVITGIE VGDASIANSL LSMFTTTTRL SAAAQREYMY RVWSPLIHIQ 790 800 810 820 830 840 DRSINTQNLP YINRVIPVTS HWDFLRGLRH HLGFTSIPGM WKAFQGWRTS QGIVDFVAHH 850 860 870 880 890 900 MADVTFPSNP ECTIFRTPDA DVVFYTFGSY VCFATPARVP YVGTPPTTIH SNTPRCMTWG 910 920 930 940 950 960 ETIALLCEVV AEFVLHFGPV ILSAANIAYL MTRGSRTEEA KGKTKHGRGM RHGHRAGVSL 970 980 990 1000 1010 1020 SDDEYDEWRD LMRDWRRDMS VNDFLMLRER SALGVDDEDE ARYRAWLEIR AMRMAGGAYT 1030 1040 1050 1060 1070 1080 HATIIGRGGV RDEIIRTAPR RAPTRPQQHY EEEAPTAIVE FTQGGDHIGY GVHIGNGNVI 1090 1100 1110 1120 1130 1140 TVTHVASTSD EVNGSAFKIT RTVGETTWVQ GPFSQLPHMQ IGSGSPVYFT TRLHPVFTIS 1150 1160 1170 1180 1190 1200 EGTFETPNIT VNGFHVRIMN GYPTKKGDCG LPYFNSNRQL VALHAGTDTQ GETKVAQRVV 1210 1220 1230 1240 1250 1260 KEVTTQDEFQ WKGLPVVKSG LDVGGMPTGT RYHRSPAWPE EQPGETHAPA PFGAGDKRYT 1270 1280 1290 1300 1310 1320 FSQTEMLVNG LKPYTEPTAG VPPQLLSRAV THVRSYIETI IGTHRSPVLT YHQACELLER 1330 1340 1350 1360 1370 1380 TTSCGPFVQG LKGDYWDEEQ QQYTGVLANH LEQAWDKANK GIAPRNAYKL ALKDELRPIE 1390 1400 1410 1420 1430 1440 KNKAGKRRLL WGCDAATTLI ATAAFKAVAT RLQVVTPMTP VAVGINMDSV QMQVMNDSLK 1450 1460 1470 1480 1490 1500 GGVLYCLDYS KWDSTQNPAV TAASLAILER FAEPHPIVSC AIEALSSPAE GYVNDIKFVT 1510 1520 1530 1540 1550 1560 RGGLPSGMPF TSVVNSINHM IYVAAAILQA YESHNVPYTG NVFQVETVHT YGDDCMYSVC 1570 1580 1590 1600 1610 1620 PATASIFHAV LANLTSYGLK PTAADKSDAI KPTNTPVFLK RTFTQTPHGV RALLDITSIT 1630 1640 1650 1660 1670 1680 RQFYWLKANR TSDPSSPPAF DRQARSAQLE NALAYASQHG PVVFDTVRQI AIKTAQGEGL 1690 1700 1710 1720 1730 1740 VLVNTNYDQA LATYNAWFIG GTVPDPVGHT EGTHKIVFEM EGNGSNPEPK QSNNPMVVDP 1750 1760 1770 1780 1790 1800 PGTTGPTTSH VVVANPEQPN GAAQRLELAV ATGAIQSNVP EAIRNCFAVF RTFAWNDRMP 1810 1820 1830 1840 1850 1860 TGTFLGSISL HPNINPYTAH LSGMWAGWGG SFEVRLSISG SGVFAGRIIA SVIPPGVDPS 1870 1880 1890 1900 1910 1920 SIRDPGVLPH AFVDARITEP VSFMIPDVRA VDYHRMDGAE PTCSLGFWVY QPLLNPFSTT 1930 1940 1950 1960 1970 1980 AVSTCWVSVE TKPGGDFDFC LLRPPGQQME NGVSPEGLLP RRLGYSRGNR VGGLVVGMVL 1990 2000 2010 2020 2030 2040 VAEHKQVNRH FNSNSVTFGW STAPVNPMAA EIVTNQAHST SRHAWLSIGA QNKGPLFPGI 2050 2060 2070 2080 2090 2100 PNHFPDSCAS TIVGAMDTSL GGRPSTGVCG PAISFQNNGD VYENDTPSVM FATYDPLTSG 2110 2120 2130 2140 2150 2160 TGVALTNSIN PASLALVRIS NNDFDTSGFA NDKNVVVQMS WEMYTGTNQI RGQVTPMSGT 2170 2180 2190 2200 2210 2220 NYTFTSTGAN TLVLWQERML SYDGHQAILY SSQLERTAEY FQNDIVNIPE NSMAVFNVET 2230 2240 2250 2260 2270 2280 NSASFQIGIR PDGYMVTGGS IGINVPLEPE TRFQYVGILP LSAALSGPSG NMGRARRVFQ
	Isoform Subgenomic capsid protein (VP1) [UniParc]. Checksum: 5B6C8A3ED75E4E3C	FASTA	561	60,113
	10 20 30 40 50 60 MEGNGSNPEP KQSNNPMVVD PPGTTGPTTS HVVVANPEQP NGAAQRLELA VATGAIQSNV 70 80 90 100 110 120 PEAIRNCFAV FRTFAWNDRM PTGTFLGSIS LHPNINPYTA HLSGMWAGWG GSFEVRLSIS 130 140 150 160 170 180 GSGVFAGRII ASVIPPGVDP SSIRDPGVLP HAFVDARITE PVSFMIPDVR AVDYHRMDGA 190 200 210 220 230 240 EPTCSLGFWV YQPLLNPFST TAVSTCWVSV ETKPGGDFDF CLLRPPGQQM ENGVSPEGLL 250 260 270 280 290 300 PRRLGYSRGN RVGGLVVGMV LVAEHKQVNR HFNSNSVTFG WSTAPVNPMA AEIVTNQAHS 310 320 330 340 350 360 TSRHAWLSIG AQNKGPLFPG IPNHFPDSCA STIVGAMDTS LGGRPSTGVC GPAISFQNNG 370 380 390 400 410 420 DVYENDTPSV MFATYDPLTS GTGVALTNSI NPASLALVRI SNNDFDTSGF ANDKNVVVQM 430 440 450 460 470 480 SWEMYTGTNQ IRGQVTPMSG TNYTFTSTGA NTLVLWQERM LSYDGHQAIL YSSQLERTAE 490 500 510 520 530 540 YFQNDIVNIP ENSMAVFNVE TNSASFQIGI RPDGYMVTGG SIGINVPLEP ETRFQYVGIL 550 560 PLSAALSGPS GNMGRARRVF Q
	Isoform Uncharacterized protein VP3 [UniParc]. See Q672I0.		–	–

References

[1]	"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: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY694184 Genomic RNA. Translation: AAU09265.2.
RefSeq	YP_077278.1. NC_006269.1.
3D structure databases
HSSP	HSSP built from PDB template 1KHV based on UniProtKB P27410.
ProteinModelPortal	Q672I1.
SMR	Q672I1. Positions 1207-1705.
ModBase	Search...
Protein family/group databases
MEROPS	C24.003.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	5176815.
Family and domain databases
InterPro	IPR004005. Calicivirus_coat. IPR004004. Helic/Pol/Pept_Calicivir-typ. IPR000605. Helicase_SF3_ssDNA/RNA_vir. IPR014759. Helicase_SF3_ssRNA_vir. IPR001665. Norovirus_pept_C37. IPR000317. Peptidase_C24. IPR001205. RNA-dir_pol_C. IPR007094. RNA-dir_pol_PSvirus. IPR009003. Trypsin-like_Pept_dom. [Graphical view]
Pfam	PF00915. 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]
PRINTS	PR00916. 2CENDOPTASE. PR00918. CALICVIRUSNS.
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	PS50507. RDRP_SSRNA_POS. 1 hit. PS51218. SF3_HELICASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_SVSAP

Accession

Primary (citable) accession number: Q672I1

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 2008
Last sequence update:	October 11, 2004
Last modified:	May 1, 2013
This is version 52 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program