ID   POLG_SMSV1              Reviewed;        1879 AA.
AC   P36286;
DT   01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT   06-JUN-2002, sequence version 3.
DT   24-JAN-2024, entry version 124.
DE   RecName: Full=Genome polyprotein;
DE   Contains:
DE     RecName: Full=Protein p16;
DE   Contains:
DE     RecName: Full=Protein p32;
DE   Contains:
DE     RecName: Full=NTPase;
DE              EC=3.6.1.15;
DE     AltName: Full=p39;
DE   Contains:
DE     RecName: Full=Protein p30;
DE   Contains:
DE     RecName: Full=Viral genome-linked protein;
DE     AltName: Full=VPg;
DE     AltName: Full=p13;
DE   Contains:
DE     RecName: Full=Protease-polymerase p76;
DE              Short=Pro-Pol;
DE              EC=2.7.7.48;
DE              EC=3.4.22.66;
GN   ORFNames=ORF1;
OS   San Miguel sea lion virus serotype 1 (SMSV-1) (SMSV serotype 1).
OC   Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC   Picornavirales; Caliciviridae; Vesivirus;
OC   Vesicular exanthema of swine virus.
OX   NCBI_TaxID=36406;
OH   NCBI_TaxID=9702; Otariidae (fur seals & sea lions).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA], AND SEQUENCE REVISION TO 724-726; 745;
RP   765 AND 774.
RA   Neill J.D., Seal B.S., Ridpath J.F.;
RL   Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 724-1879.
RX   PubMed=7769708; DOI=10.1128/jvi.69.7.4484-4488.1995;
RA   Neill J.D., Meyer R.F., Seal B.S.;
RT   "Genetic relatedness of the caliciviruses: San Miguel sea lion and
RT   vesicular exanthema of swine viruses constitute a single genotype within
RT   the Caliciviridae.";
RL   J. Virol. 69:4484-4488(1995).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1841-1879.
RX   PubMed=1529644; DOI=10.1016/0168-1702(92)90008-w;
RA   Neill J.D.;
RT   "Nucleotide sequence of the capsid protein gene of two serotypes of San
RT   Miguel sea lion virus: identification of conserved and non-conserved amino
RT   acid sequences among calicivirus capsid proteins.";
RL   Virus Res. 24:211-222(1992).
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 p76 processes the polyprotein: Pro-Pol is
CC       first released by autocleavage, then all other proteins are cleaved.
CC       Cleaves host translation initiation factor eIF4G1 and eIF4G2 thereby
CC       inducing a shutdown of host protein synthesis. This shutdown may not
CC       prevent viral mRNA from being translated since viral Vpg replaces the
CC       cap. May cleave host polyadenylate-binding protein thereby inhibiting
CC       cellular translation. It is also an RNA-directed RNA polymerase which
CC       replicates genomic and antigenomic viral RNA by recognizing specific
CC       signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis
CC       internally on antigenomic RNA. This sgRNA codes for structural
CC       proteins. Catalyzes the covalent attachment VPg with viral RNAs (By
CC       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: [Protein p32]: Homodimer (By similarity). Interacts with
CC       NTPase, protein p30 and protease-polymerase p76 (By similarity).
CC       {ECO:0000250|UniProtKB:Q66914}.
CC   -!- SUBUNIT: [Viral genome-linked protein]: Interacts with capsid protein
CC       VP1 and protease-polymerase p76 (By similarity).
CC       {ECO:0000250|UniProtKB:Q66914}.
CC   -!- SUBUNIT: [Protease-polymerase p76]: Homooligomer (By similarity).
CC       Interacts with Vpg, protein p32 and may interact with capsid protein
CC       VP1 (By similarity). {ECO:0000250|UniProtKB:Q66914}.
CC   -!- DOMAIN: Protease-polymerase is composed of two domains displaying two
CC       different catalytic activity. These activities may act independently
CC       (By similarity). {ECO:0000250}.
CC   -!- PTM: Specific enzymatic cleavages in vivo yield mature proteins. Pro-
CC       Pol is first autocatalytically cleaved, then processes the whole
CC       polyprotein (By similarity). {ECO:0000250}.
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}.
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DR   EMBL; U15301; AAA96501.2; -; Genomic_RNA.
DR   EMBL; M87481; AAA16216.1; -; Unassigned_DNA.
DR   SMR; P36286; -.
DR   Proteomes; UP000007224; Genome.
DR   Proteomes; UP000159168; Genome.
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:ribonucleoside triphosphate phosphatase activity; IEA:UniProtKB-EC.
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-dependent RNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006351; P:DNA-templated transcription; IEA:InterPro.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR   CDD; cd00009; AAA; 1.
DR   CDD; cd23192; Caliciviridae_RdRp; 1.
DR   Gene3D; 1.10.260.110; -; 1.
DR   Gene3D; 1.20.960.20; -; 1.
DR   Gene3D; 3.30.70.270; -; 1.
DR   Gene3D; 6.10.140.320; -; 1.
DR   Gene3D; 6.10.250.3230; -; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR   InterPro; IPR016024; ARM-type_fold.
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; IPR027417; P-loop_NTPase.
DR   InterPro; IPR000317; Peptidase_C24.
DR   InterPro; IPR009003; Peptidase_S1_PA.
DR   InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR   InterPro; IPR001205; RNA-dir_pol_C.
DR   InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR   InterPro; IPR049434; VPg.
DR   Pfam; PF03510; Peptidase_C24; 1.
DR   Pfam; PF00680; RdRP_1; 1.
DR   Pfam; PF00910; RNA_helicase; 1.
DR   Pfam; PF20915; VPg; 1.
DR   PRINTS; PR00916; 2CENDOPTASE.
DR   PRINTS; PR00918; CALICVIRUSNS.
DR   SUPFAM; SSF48371; ARM repeat; 1.
DR   SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR   SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR   SUPFAM; SSF50494; Trypsin-like serine proteases; 1.
DR   PROSITE; PS51894; CV_3CL_PRO; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
DR   PROSITE; PS51218; SF3_HELICASE_2; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Covalent protein-RNA linkage; Hydrolase; Nucleotide-binding;
KW   Nucleotidyltransferase; Phosphoprotein; Protease;
KW   RNA-directed RNA polymerase; Thiol protease; Transferase;
KW   Viral RNA replication.
FT   CHAIN           1..1879
FT                   /note="Genome polyprotein"
FT                   /id="PRO_0000342015"
FT   CHAIN           1..148
FT                   /note="Protein p16"
FT                   /id="PRO_0000342016"
FT   CHAIN           149..435
FT                   /note="Protein p32"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036928"
FT   CHAIN           436..791
FT                   /note="NTPase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036929"
FT   CHAIN           792..1070
FT                   /note="Protein p30"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036930"
FT   CHAIN           1071..1183
FT                   /note="Viral genome-linked protein"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036931"
FT   CHAIN           1184..1879
FT                   /note="Protease-polymerase p76"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036932"
FT   DOMAIN          564..720
FT                   /note="SF3 helicase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT   DOMAIN          1188..1341
FT                   /note="Peptidase C24"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   DOMAIN          1591..1716
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          37..98
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        38..54
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        77..96
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        1222
FT                   /note="For 3CLpro activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   ACT_SITE        1243
FT                   /note="For 3CLpro activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   ACT_SITE        1305
FT                   /note="For 3CLpro activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01242"
FT   BINDING         590..597
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT   SITE            148..149
FT                   /note="Cleavage; by Pro-Pol"
FT                   /evidence="ECO:0000250"
FT   SITE            435..436
FT                   /note="Cleavage; by Pro-Pol"
FT                   /evidence="ECO:0000250"
FT   SITE            791..792
FT                   /note="Cleavage; by Pro-Pol"
FT                   /evidence="ECO:0000250"
FT   SITE            1070..1071
FT                   /note="Cleavage; by Pro-Pol"
FT                   /evidence="ECO:0000250"
FT   SITE            1183..1184
FT                   /note="Cleavage; by Pro-Pol"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         1093
FT                   /note="O-(5'-phospho-RNA)-tyrosine"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1879 AA;  209295 MW;  B03F7FE91FC73F53 CRC64;
     MAQTLSKISN KENASVGLWP KRFKPHQPTP TWMVRCGPLD HDSRHGRDPV RASPQAKRVR
     TPNPYPRHLK PAASAVVRSG TNPSHLKPTS TDVVRSGPET PCCEAKDGGV VRSCKTCNLK
     PAHDSKAVSF FPAQTDGLTG DEPEFIAEAC PSCVLYDTCP NCTSRAINDD GSTDGTIPSW
     DQIETTPAFL SLLSNTDEEM SADELTNLAA HLRKAFETGS HPPNVDYSKD QLQGLLEMAE
     AALPPARRQT LPFYQQRLEA RRTWREKIFN LPLDELSKIL TTSKDRFQRC AAWKVVLEKA
     VLAKEYGEEA YAYAQEALKN INSFDVNLVL KMAAGTFIGH LRMMTVDNPD MVSYLPKLIV
     KLKPLTLKMI IDNHENTKEG WLVTLTSLAE LYGMVEVAID FVPTVIGNLF DLLMKTTSKV
     YSMFKSVILA TFTSESLDFT NPFWYAIAAI LCFLITGAIP HNGKMKIIKN ILSNATGIVA
     GVKAIQTLGA MFSTWSNERL VNDLSSRTIA ITELNNPTIT ADIDAVINLQ RLAETLREEV
     KSHTLNPLMQ PYTPILRNLM SALDNVISCC TRRKAIATKR TAPVAVILTG PPGCGKTTAA
     FALAKRLSQQ KPSIISLDVD HHDTYTGNEV CIIDEFDSSD KVDYANFVVN MVNTNPMVLN
     CDLVENKGKT FRSKYVIMKS NSETPVKPTS RRAGAFYRRV MIVDVKNTAV ENWKRENPGK
     PVPKWCFNKD FSHLHLSMRG TEAYWREYVL DPTGRNHQSQ KAPPDQHVTL EQLDQKMVVQ
     HTTNTSEFVT QAGEVPVFGF VCQNNEIDTV YNLLAAVKAR YGANFNLYKG MTRTAHENSG
     CGAHVHVISR EDNFRGKAFT VNRSRLESVP HLEGDSFRRS LGVVMSDKDV TTMFYYIKGK
     VINDQVNLTE LPANQHVVTV HTVYDMAWAL RRHLKWTGQW QLIKAAYEIM CYPDTAACAL
     RNWMDSTDFS EEHVVTQFIA PGGTIILESC YGARMWATGQ RLIRAGGLTE AGGPQGGVRF
     AGLGARNVPW SEILREFMTL ISHIWSQIKG ATVVLTALTF YLKRFRPRVE AKGKNKNKGP
     RKNTGVALTD DEYDEWRQYK AEKKLDLTVE DFLQLRHRAA MGADDTDAVK FRCWYSERQR
     NYHDLEDVTI IGRGGVKREL IRKGPLRPRG NDFYDEPDDW YSEGVIDGVT HKNAIVSVDD
     VDGMHKGYAL HIGHGVYMSL KHVVSGNAKI LSEEPKNLTF NGELATFRLN TTLPTAAPVG
     TSKPIKDPWG NPVSTDWQFK NYNTTSGNIY GACGSSCSLT RQGDCGLPYV DDHGVVVGLH
     AGSGGDKCPS RKLIVPYVKV DMRIRDTCTK EYYKDNVPMI SYKGLLVKET GEPRTIMKGT
     RLHVSPAHTD DYEECTHQPA SLGAGDPRCP MSLTGIMVNN LQPYTEAPRT DTATLNRVTK
     MLISHMEGYV PKIHKTEEDM ISAFYMLNHD TSCGPYIGGR KKDHVKDGVL DKNLLDLLSS
     KWNRAKCGLA LPHEYALGLK DELRPKDKVA VGKRRLIWGC DVGVSTVCRA AFKRVSESIM
     ANHALGFIQV GINMDGPAVE DPFKRLERPK HDRYCVDYSK WDSTQPPKVT SQSIDILRHF
     TDKSPIVDSA CATLKSNPIG IFNGVAFKVA GGLPSGMPLT SIINSLNHCL MVGSAVVKAL
     EDSGVQVTWN IFDSMDLFTY GDDGVYIVPP LISSVMPKVF SNLRQFGLKP TRTDKTDAEI
     TPIPADEPVE FLKRTIVRTE NGVRALLDKS SIIRQFYYIK AENTENWTVP PKKIDTSSRG
     QQLYNAGLYA SQHGEEFYTN KIIPLVQRAI EFEGLHIEVP EFHQAVQAYN GYFNGTEDQP
     SQIALASGGT GFGGEVFEN
//