POLG_SMSV1
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 03-AUG-2022, entry version 118.
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.
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: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: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 Gene3D; 3.30.70.270; -; 1.
DR Gene3D; 3.40.50.300; -; 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 Pfam; PF03510; Peptidase_C24; 1.
DR Pfam; PF00680; RdRP_1; 1.
DR Pfam; PF00910; RNA_helicase; 1.
DR PRINTS; PR00916; 2CENDOPTASE.
DR PRINTS; PR00918; CALICVIRUSNS.
DR SUPFAM; SSF48371; SSF48371; 1.
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 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
