POLG_SVM93
ID POLG_SVM93 Reviewed; 2208 AA.
AC Q69014;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Genome polyprotein;
DE Contains:
DE RecName: Full=Protein p28;
DE Contains:
DE RecName: Full=NTPase;
DE EC=3.6.1.15;
DE AltName: Full=p35;
DE Contains:
DE RecName: Full=Protein p32;
DE Contains:
DE RecName: Full=Viral genome-linked protein;
DE AltName: Full=VPg;
DE AltName: Full=p14;
DE Contains:
DE RecName: Full=Protease-polymerase p70;
DE Short=Pro-Pol;
DE EC=2.7.7.48;
DE EC=3.4.22.66;
DE Contains:
DE RecName: Full=Capsid protein;
DE Short=CP;
DE AltName: Full=VP1;
DE AltName: Full=p60;
DE Flags: Fragment;
GN ORFNames=ORF1;
OS Sapporo virus (strain Human/United Kingdom/Manchester/1993)
OS (Hu/SV/Man/1993/UK).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC Picornavirales; Caliciviridae; Sapovirus.
OX NCBI_TaxID=82659;
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=7661689; DOI=10.1007/bf01322662;
RA Liu B.L., Clarke I.N., Caul E.O., Lambden P.R.;
RT "Human enteric caliciviruses have a unique genome structure and are
RT distinct from the Norwalk-like viruses.";
RL Arch. Virol. 140:1345-1356(1995).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1135-1649.
RX PubMed=17121797; DOI=10.1128/jvi.01462-06;
RA Fullerton S.W., Blaschke M., Coutard B., Gebhardt J., Gorbalenya A.,
RA Canard B., Tucker P.A., Rohayem J.;
RT "Structural and functional characterization of sapovirus RNA-dependent RNA
RT polymerase.";
RL J. Virol. 81:1858-1871(2007).
CC -!- FUNCTION: NTPase presumably plays a role in replication. Despite having
CC similarities with helicases, does not seem to display any helicase
CC activity (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Viral genome-linked protein is covalently linked to the 5'-
CC end of the positive-strand, negative-strand genomic RNAs and subgenomic
CC RNA. Acts as a genome-linked replication primer. May recruit ribosome
CC to viral RNA thereby promoting viral proteins translation (By
CC similarity). {ECO:0000250}.
CC -!- FUNCTION: Protease-polymerase processes the polyprotein: Pro-Pol is
CC first released by autocleavage, then all other proteins are cleaved.
CC {ECO:0000250}.
CC -!- FUNCTION: Protease-polymerase is an RNA-directed RNA polymerase which
CC replicates genomic and antigenomic viral RNA by recognizing specific
CC signals. Catalyzes the covalent attachment VPg with viral RNAs (By
CC similarity). {ECO:0000250}.
CC -!- FUNCTION: Capsid protein self assembles to form an icosahedral capsid
CC with a T=3 symmetry, about 38 nm in diameter, and consisting of 180
CC capsid proteins. The capsid encapsulate the genomic RNA and VP2
CC proteins. Attaches virion to target cells, inducing endocytosis of the
CC viral particle. Acidification of the endosome induces conformational
CC change of capsid protein thereby injecting virus genomic RNA into host
CC cytoplasm (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-
CC diphosphate + H(+) + phosphate; Xref=Rhea:RHEA:23680,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:61557; EC=3.6.1.15;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endopeptidase with a preference for cleavage when the P1
CC position is occupied by Glu-|-Xaa and the P1' position is occupied by
CC Gly-|-Yaa.; EC=3.4.22.66; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU01242};
CC -!- SUBUNIT: [Capsid protein]: Homodimer. Homomultimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: [Capsid protein]: Virion. Host cytoplasm.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative promoter usage, Alternative initiation; Named isoforms=3;
CC Name=Genome polyprotein;
CC IsoId=Q69014-1; Sequence=Displayed;
CC Name=Subgenomic capsid protein; Synonyms=VP1;
CC IsoId=Q69014-2; Sequence=VSP_034384;
CC Name=Uncharacterized protein VP3;
CC IsoId=Q69015-1; Sequence=External;
CC -!- DOMAIN: Protease-polymerase is composed of two domains displaying two
CC different catalytic activity. These activities may act independently.
CC -!- PTM: Specific enzymatic cleavages in vivo yield mature proteins. Pro-
CC Pol is first autocatalytically cleaved, then processes the whole
CC polyprotein.
CC -!- PTM: VPg is uridylylated by the polymerase and is covalently attached
CC to the 5'-end of the polyadenylated genomic and subgenomic RNAs. This
CC uridylylated form acts as a nucleotide-peptide primer for the
CC polymerase (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: Two different RNAs lead the expression of the capsid
CC protein. One arises from the cleavage of the polyprotein translated
CC from the genomic RNA and the other from the translation of a subgenomic
CC RNA derived from the (-)RNA template. Capsid protein expressed from the
CC subgenomic mRNA is produced in much larger amounts than the cleaved one
CC (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: [Isoform Genome polyprotein]: Produced from the genomic
CC RNA.
CC -!- MISCELLANEOUS: [Isoform Subgenomic capsid protein]: Produced from the
CC subgenomic RNA by alternative promoter usage. {ECO:0000305}.
CC -!- CAUTION: The N-terminal part of the polyprotein may be missing and the
CC genome sequence may lack the 5'-end, since all other sapoviruses code
CC for a supplemental N-terminal peptide. {ECO:0000305}.
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DR EMBL; X86560; CAA60262.1; -; Genomic_RNA.
DR PDB; 2CKW; X-ray; 2.30 A; A=1135-1649.
DR PDB; 2UUT; X-ray; 2.40 A; A=1135-1649.
DR PDB; 2UUW; X-ray; 2.76 A; A=1135-1649.
DR PDB; 2WK4; X-ray; 2.98 A; A/B=1135-1649.
DR PDBsum; 2CKW; -.
DR PDBsum; 2UUT; -.
DR PDBsum; 2UUW; -.
DR PDBsum; 2WK4; -.
DR SMR; Q69014; -.
DR MEROPS; C24.003; -.
DR PRIDE; Q69014; -.
DR EvolutionaryTrace; Q69014; -.
DR Proteomes; UP000113838; Genome.
DR GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0019028; C:viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR GO; GO:0017111; F:nucleoside-triphosphatase activity; IEA:RHEA.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0003724; F:RNA helicase activity; IEA:InterPro.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR CDD; cd00205; rhv_like; 1.
DR Gene3D; 2.60.120.20; -; 1.
DR Gene3D; 3.30.70.270; -; 2.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR004005; Calicivirus_coat.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR004004; Helic/Pol/Pept_Calicivir-typ.
DR InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir.
DR InterPro; IPR014759; Helicase_SF3_ssRNA_vir.
DR InterPro; IPR001665; Norovirus_pept_C37.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000317; Peptidase_C24.
DR InterPro; IPR009003; Peptidase_S1_PA.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR033703; Rhv-like.
DR InterPro; IPR001205; RNA-dir_pol_C.
DR InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR InterPro; IPR029053; Viral_coat.
DR Pfam; PF00915; Calici_coat; 1.
DR Pfam; PF03510; Peptidase_C24; 1.
DR Pfam; PF05416; Peptidase_C37; 1.
DR Pfam; PF00680; RdRP_1; 1.
DR Pfam; PF00910; RNA_helicase; 1.
DR PRINTS; PR00916; 2CENDOPTASE.
DR PRINTS; PR00918; CALICVIRUSNS.
DR SUPFAM; SSF50494; SSF50494; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS51894; CV_3CL_PRO; 1.
DR PROSITE; PS50507; RDRP_SSRNA_POS; 1.
DR PROSITE; PS51218; SF3_HELICASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative initiation; Alternative promoter usage;
KW ATP-binding; Capsid protein; Covalent protein-RNA linkage; DNA replication;
KW Host cytoplasm; Hydrolase; Nucleotide-binding; Nucleotidyltransferase;
KW Phosphoprotein; Protease; RNA-directed RNA polymerase; Thiol protease;
KW Transferase; Viral RNA replication; Virion.
FT CHAIN <1..2208
FT /note="Genome polyprotein"
FT /id="PRO_0000341624"
FT CHAIN 1..252
FT /note="Protein p28"
FT /evidence="ECO:0000250"
FT /id="PRO_0000036921"
FT CHAIN 253..593
FT /note="NTPase"
FT /evidence="ECO:0000250"
FT /id="PRO_0000036922"
FT CHAIN 594..867
FT /note="Protein p32"
FT /evidence="ECO:0000250"
FT /id="PRO_0000036923"
FT CHAIN 868..981
FT /note="Viral genome-linked protein"
FT /evidence="ECO:0000250"
FT /id="PRO_0000036924"
FT CHAIN 982..1649
FT /note="Protease-polymerase p70"
FT /evidence="ECO:0000250"
FT /id="PRO_0000036926"
FT CHAIN 1650..2208
FT /note="Capsid protein"
FT /evidence="ECO:0000250"
FT /id="PRO_0000036927"
FT DOMAIN 382..536
FT /note="SF3 helicase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT DOMAIN 982..1130
FT /note="Peptidase C24"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT DOMAIN 1370..1495
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT REGION 1650..1674
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1653..1674
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 1012
FT /note="For 3CLpro activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT ACT_SITE 1033
FT /note="For 3CLpro activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT ACT_SITE 1097
FT /note="For 3CLpro activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT BINDING 408..415
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT SITE 252..253
FT /note="Cleavage; by Pro-Pol"
FT /evidence="ECO:0000250"
FT SITE 593..594
FT /note="Cleavage; by Pro-Pol"
FT /evidence="ECO:0000250"
FT SITE 867..868
FT /note="Cleavage; by Pro-Pol"
FT /evidence="ECO:0000250"
FT SITE 981..982
FT /note="Cleavage; by Pro-Pol"
FT /evidence="ECO:0000250"
FT SITE 1649..1650
FT /note="Cleavage; by Pro-Pol"
FT /evidence="ECO:0000250"
FT MOD_RES 893
FT /note="O-(5'-phospho-RNA)-tyrosine"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..1647
FT /note="Missing (in isoform Subgenomic capsid protein)"
FT /evidence="ECO:0000305"
FT /id="VSP_034384"
FT NON_TER 1
FT STRAND 1137..1139
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1142..1146
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1157..1162
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1175..1177
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1181..1183
FT /evidence="ECO:0007829|PDB:2CKW"
FT TURN 1185..1187
FT /evidence="ECO:0007829|PDB:2UUW"
FT HELIX 1191..1199
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1200..1203
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1211..1229
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1239..1245
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1248..1251
FT /evidence="ECO:0007829|PDB:2UUW"
FT STRAND 1254..1256
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1260..1263
FT /evidence="ECO:0007829|PDB:2CKW"
FT TURN 1266..1268
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1273..1287
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1295..1300
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1303..1306
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1307..1311
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1317..1321
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1323..1341
FT /evidence="ECO:0007829|PDB:2CKW"
FT TURN 1342..1345
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1346..1349
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1358..1365
FT /evidence="ECO:0007829|PDB:2CKW"
FT TURN 1366..1369
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1370..1373
FT /evidence="ECO:0007829|PDB:2CKW"
FT TURN 1378..1380
FT /evidence="ECO:0007829|PDB:2UUW"
FT HELIX 1381..1383
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1386..1397
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1405..1414
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1418..1421
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1424..1427
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1429..1431
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1439..1461
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1470..1473
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1474..1479
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1482..1487
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1489..1493
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1495..1504
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1511..1513
FT /evidence="ECO:0007829|PDB:2WK4"
FT STRAND 1521..1523
FT /evidence="ECO:0007829|PDB:2UUT"
FT STRAND 1529..1534
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1537..1542
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1544..1552
FT /evidence="ECO:0007829|PDB:2CKW"
FT STRAND 1553..1560
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1570..1585
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1589..1606
FT /evidence="ECO:0007829|PDB:2CKW"
FT HELIX 1615..1628
FT /evidence="ECO:0007829|PDB:2CKW"
SQ SEQUENCE 2208 AA; 242737 MW; 3E299D5BA20E45DC CRC64;
MFGTKAPDSV QEGTLFRELF GVDQTEQFPL SLADLARLQG ELVDATRTPG HALRQKYTMT
TIQDLINKIT KVVPVQATLN EMHARRQFER ERADLFHELP LVDEDAVAQP KTYFYTMWRQ
VVKKGKAYFC PLVKTSAWRT KISAITEPIK DFLIAFWQAV QQEMGVNPQY LQLAWLQKLK
PTTLTIILQQ HKHTVSGWLA TMTALVEVYS NLFDDLRKSS VTIVSSIGAF FDICKDFVSQ
VVELVKTTFT AQGPTDLGWA AVLAGAAMIL LKMSGCPGVI GMWTKVLKIC GGITTITAAA
RGVRWLKDLY EEAEGRRLPK MYMARGAALI ELAASREVTG VDELKGLLDC FTILIEEGTE
LIHKFGTSPL AGLVRTYVSE LETQANNIRS TIKLDTPRRV PVVIILTGAP GIGKTRLAQY
IGQRFGKTSN FSVAVDHHDG YTGNTVCIWD EFDVDSKGAF VETMIGIANT APFPLNCDRV
ENKGRVFTSD YVICTSNYPT SVIPDNPRAA AFYRRVLTVD VSAPDLEEWK KRNPGKRPTP
DLYQDDFSHL KLMLRPYLGY NPDGDTLEGP RVAPTQISIA GLITLMERRF KEQAGPLQNL
WLQVPKTLVE QSTNMVKAFM YANRAVCDVI PNPATRDITE TALSKVFVCG TAPPPEFVGK
HIVITGIEVG DASIANSLLS MFTTTTRLSA AAQREYMYRV WSPLIHIQDR SMNTQNLPYI
NRVIPVTSHW DFLRGLRHHL GFTSIPGMWK AFQGWRTSQG IVDFVAHHMA DVTFPSNPEC
TIFRTPDADV VFYTFGSYVC FATPARVPYV GTPPTTIHSN TPRCMTWGET LALLCEVVAE
FVLHFGPVIL SAANIAYLMT RGSRTEEAKG KTKHGRGMRH GHRAGVSLSD DEYDEWRDLM
RDWRRDMSVN DFLMLRERSA LGMDDEDVAR YRAWLEIRAM RMAGGAYTHA TIIGRGGVRD
EIIRTSPRRA PTRPQQHYEE EGPTAIVEFT QGGDHIGYGV HIGNGNVITV THVASTSDEV
NGSAFKITRT VGETTWVQGP FSQLPHMQIG SGSPVYFTTR LHPVFTISEG TFETPNITVN
GFHVRIMNGY PTKKGDCGLP YFNSNRQLVA LHAGTDTQGE TKVAQRVVKE VTTQDEFQWK
GLPVVKSGLD VGGMPTGTRY HRSPAWPEEQ PGETHAPAPF GSGDKRYTFS QTEMLVNGLK
PYTEPTAGVP PQLLSRAVTH VRSYIETIIG THRSPVLTYH QACELLERTT SCGPFVQGLK
GDYWDEEQQQ YTGVLANHLE QAWDKANKGI APRNAYKLAL KDELRPIEKN KAGKRRLLWG
CDAATTLIAT AAFKAVATRL QVVTPMTPVA VGINMDSVQM QVMNDSLKGG VLYCLDYSKW
DSTQNPAVTA ASLAILERFA EPHPIVSCAI EALSSPAEGY VNDIKFVTRG GLPSGMPFTS
VVNSINHMIY VAAAILQAYE SHNVPYTGNV FQVETIHTYG DDCMYSVCPA TASIFHTVLA
NLTSYGLKPT AADKSDAIKP TNTPVFLKRT FTQTPHGIRA LLDITSITRQ FYWLKANRTS
DPSSPPAFDR QARSAQLENA LAYASQHGPV MFDTVRQIAI KTAQGEGLVL VNTNYDQALA
TYNAWFIGGT VPDPVGHTEG THKIVFEMEG NGSNPEPKQS NNPMVVDPPG TTGPTTSHVV
VANPEQPNGA AQRLELAVAT GAIQSNVPEA IRNCFAVFRT FAWNDRMPTG TFLGSISLHP
NINPYTSHLS GMWAGWGGSF EVRLSISGSG VFAGRIIASV IPPGVDPSSI RDPGVLPHAF
VDARITEPVS FMIPDVRAVD YHRMDGAEPT CSLGFWVYQP LLNPFSTTAV STCWVSVETK
PGGDFDFCLL RPPGQQMENG VSPEGLLPRR LGYSRGNRVG GLVVGMILVA EHKQVNRHFN
SNSVTFGWST APVNPMAAEI VTNQAHSTSR HAWLSIGAQN KGPLFPGIPN HFPDSCASTV
VGAMDTSLGG RPSTGVCGPA ISFQNNGDVY ENDTPSVMFA TYDPLTSGTG VALTNSINPA
SLALVRISNN DFDTSGFAND KNVVVQMSWE MYTGTNQIRG QVTPMSGTNY TFTSTGANTL
VLWQERMLSY DGHQAILYSS QLERTAEYFQ NDIVNIPENS MAVFNVETNS ASFQIGIRPD
GYMVTGGSIG VNVPLEPETR FQYVGILPLS AALSGPSGNM GRARRVFQ
