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P36286

- POLG_SMSV1

UniProt

P36286 - POLG_SMSV1

Protein

Genome polyprotein

Gene

ORF1

Organism
San Miguel sea lion virus serotype 1 (SMSV-1) (SMSV serotype 1)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 3 (06 Jun 2002)
      Previous versions | rss
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    Functioni

    NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity By similarity.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.By similarity
    Protease-polymerase p76 processes the polyprotein: Pro-Pol is first released by autocleavage, then all other proteins are cleaved. Cleaves host translation initiation factor eIF4G1 and eIF4G2 thereby inducing a shutdown of host protein synthesis. This shutdown may not prevent viral mRNA from being translated since viral Vpg replaces the cap. May cleave host polyadenylate-binding protein thereby inhibiting cellular translation. It is also an RNA-directed RNA polymerase which replicates genomic and antigenomic viral RNA by recognizing specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs By similarity.By similarity

    Catalytic activityi

    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).PROSITE-ProRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei148 – 1492Cleavage; by Pro-PolBy similarity
    Sitei435 – 4362Cleavage; by Pro-PolBy similarity
    Sitei791 – 7922Cleavage; by Pro-PolBy similarity
    Sitei1070 – 10712Cleavage; by Pro-PolBy similarity
    Sitei1183 – 11842Cleavage; by Pro-PolBy similarity
    Active sitei1222 – 12221For protease activityBy similarity
    Active sitei1243 – 12431For protease activityBy similarity
    Active sitei1305 – 13051For protease activityBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi590 – 5978ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. cysteine-type endopeptidase activity Source: InterPro
    3. RNA binding Source: InterPro
    4. RNA-directed RNA polymerase activity Source: UniProtKB-KW
    5. RNA helicase activity Source: InterPro

    GO - Biological processi

    1. RNA-protein covalent cross-linking Source: UniProtKB-KW
    2. transcription, DNA-templated Source: InterPro
    3. viral RNA genome replication Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

    Keywords - Biological processi

    Viral RNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Genome polyprotein
    Cleaved into the following 6 chains:
    Alternative name(s):
    p39
    Alternative name(s):
    VPg
    p13
    Protease-polymerase p76 (EC:2.7.7.48, EC:3.4.22.66)
    Short name:
    Pro-Pol
    Gene namesi
    ORF Names:ORF1
    OrganismiSan Miguel sea lion virus serotype 1 (SMSV-1) (SMSV serotype 1)
    Taxonomic identifieri36406 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
    Virus hostiOtariidae (fur seals & sea lions) [TaxID: 9702]
    ProteomesiUP000007224: Genome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 18791879Genome polyproteinPRO_0000342015Add
    BLAST
    Chaini1 – 148148Protein p16PRO_0000342016Add
    BLAST
    Chaini149 – 435287Protein p32By similarityPRO_0000036928Add
    BLAST
    Chaini436 – 791356NTPaseBy similarityPRO_0000036929Add
    BLAST
    Chaini792 – 1070279Protein p30By similarityPRO_0000036930Add
    BLAST
    Chaini1071 – 1183113Viral genome-linked proteinBy similarityPRO_0000036931Add
    BLAST
    Chaini1184 – 1879696Protease-polymerase p76By similarityPRO_0000036932Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1093 – 10931O-(5'-phospho-RNA)-tyrosineBy similarity

    Post-translational modificationi

    Specific enzymatic cleavages in vivo yield mature proteins. Pro-Pol is first autocatalytically cleaved, then processes the whole polyprotein By similarity.By similarity
    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.By similarity

    Keywords - PTMi

    Covalent protein-RNA linkage, Phosphoprotein

    Interactioni

    Subunit structurei

    Protein p32: homodimer, interacts with NTPase, protein p30 and Pro-Pol. Viral genome-linked protein interacts with capsid protein and Pro-Pol. Protease-polymerase p76: Homooligomers, interacts with Vpg, protein p32 and may interact with capsid protein By similarity.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliP36286.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini564 – 720157SF3 helicasePROSITE-ProRule annotationAdd
    BLAST
    Domaini1207 – 1311105Peptidase C24Add
    BLAST
    Domaini1591 – 1716126RdRp catalyticPROSITE-ProRule annotationAdd
    BLAST

    Domaini

    Protease-polymerase is composed of two domains displaying two different catalytic activity. These activities may act independently By similarity.By similarity

    Sequence similaritiesi

    Contains 1 peptidase C24 domain.Curated
    Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
    Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

    Family and domain databases

    Gene3Di3.40.50.300. 5 hits.
    InterProiIPR003593. AAA+_ATPase.
    IPR016024. ARM-type_fold.
    IPR004004. Helic/Pol/Pept_Calicivir-typ.
    IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR014759. Helicase_SF3_ssRNA_vir.
    IPR027417. P-loop_NTPase.
    IPR000317. Peptidase_C24.
    IPR001205. RNA-dir_pol_C.
    IPR007094. RNA-dir_pol_PSvirus.
    IPR009003. Trypsin-like_Pept_dom.
    [Graphical view]
    PfamiPF03510. Peptidase_C24. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view]
    PRINTSiPR00916. 2CENDOPTASE.
    PR00918. CALICVIRUSNS.
    SMARTiSM00382. AAA. 1 hit.
    [Graphical view]
    SUPFAMiSSF48371. SSF48371. 1 hit.
    SSF50494. SSF50494. 1 hit.
    SSF52540. SSF52540. 1 hit.
    PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P36286-1 [UniParc]FASTAAdd to Basket

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    MAQTLSKISN KENASVGLWP KRFKPHQPTP TWMVRCGPLD HDSRHGRDPV     50
    RASPQAKRVR TPNPYPRHLK PAASAVVRSG TNPSHLKPTS TDVVRSGPET 100
    PCCEAKDGGV VRSCKTCNLK PAHDSKAVSF FPAQTDGLTG DEPEFIAEAC 150
    PSCVLYDTCP NCTSRAINDD GSTDGTIPSW DQIETTPAFL SLLSNTDEEM 200
    SADELTNLAA HLRKAFETGS HPPNVDYSKD QLQGLLEMAE AALPPARRQT 250
    LPFYQQRLEA RRTWREKIFN LPLDELSKIL TTSKDRFQRC AAWKVVLEKA 300
    VLAKEYGEEA YAYAQEALKN INSFDVNLVL KMAAGTFIGH LRMMTVDNPD 350
    MVSYLPKLIV KLKPLTLKMI IDNHENTKEG WLVTLTSLAE LYGMVEVAID 400
    FVPTVIGNLF DLLMKTTSKV YSMFKSVILA TFTSESLDFT NPFWYAIAAI 450
    LCFLITGAIP HNGKMKIIKN ILSNATGIVA GVKAIQTLGA MFSTWSNERL 500
    VNDLSSRTIA ITELNNPTIT ADIDAVINLQ RLAETLREEV KSHTLNPLMQ 550
    PYTPILRNLM SALDNVISCC TRRKAIATKR TAPVAVILTG PPGCGKTTAA 600
    FALAKRLSQQ KPSIISLDVD HHDTYTGNEV CIIDEFDSSD KVDYANFVVN 650
    MVNTNPMVLN CDLVENKGKT FRSKYVIMKS NSETPVKPTS RRAGAFYRRV 700
    MIVDVKNTAV ENWKRENPGK PVPKWCFNKD FSHLHLSMRG TEAYWREYVL 750
    DPTGRNHQSQ KAPPDQHVTL EQLDQKMVVQ HTTNTSEFVT QAGEVPVFGF 800
    VCQNNEIDTV YNLLAAVKAR YGANFNLYKG MTRTAHENSG CGAHVHVISR 850
    EDNFRGKAFT VNRSRLESVP HLEGDSFRRS LGVVMSDKDV TTMFYYIKGK 900
    VINDQVNLTE LPANQHVVTV HTVYDMAWAL RRHLKWTGQW QLIKAAYEIM 950
    CYPDTAACAL RNWMDSTDFS EEHVVTQFIA PGGTIILESC YGARMWATGQ 1000
    RLIRAGGLTE AGGPQGGVRF AGLGARNVPW SEILREFMTL ISHIWSQIKG 1050
    ATVVLTALTF YLKRFRPRVE AKGKNKNKGP RKNTGVALTD DEYDEWRQYK 1100
    AEKKLDLTVE DFLQLRHRAA MGADDTDAVK FRCWYSERQR NYHDLEDVTI 1150
    IGRGGVKREL IRKGPLRPRG NDFYDEPDDW YSEGVIDGVT HKNAIVSVDD 1200
    VDGMHKGYAL HIGHGVYMSL KHVVSGNAKI LSEEPKNLTF NGELATFRLN 1250
    TTLPTAAPVG TSKPIKDPWG NPVSTDWQFK NYNTTSGNIY GACGSSCSLT 1300
    RQGDCGLPYV DDHGVVVGLH AGSGGDKCPS RKLIVPYVKV DMRIRDTCTK 1350
    EYYKDNVPMI SYKGLLVKET GEPRTIMKGT RLHVSPAHTD DYEECTHQPA 1400
    SLGAGDPRCP MSLTGIMVNN LQPYTEAPRT DTATLNRVTK MLISHMEGYV 1450
    PKIHKTEEDM ISAFYMLNHD TSCGPYIGGR KKDHVKDGVL DKNLLDLLSS 1500
    KWNRAKCGLA LPHEYALGLK DELRPKDKVA VGKRRLIWGC DVGVSTVCRA 1550
    AFKRVSESIM ANHALGFIQV GINMDGPAVE DPFKRLERPK HDRYCVDYSK 1600
    WDSTQPPKVT SQSIDILRHF TDKSPIVDSA CATLKSNPIG IFNGVAFKVA 1650
    GGLPSGMPLT SIINSLNHCL MVGSAVVKAL EDSGVQVTWN IFDSMDLFTY 1700
    GDDGVYIVPP LISSVMPKVF SNLRQFGLKP TRTDKTDAEI TPIPADEPVE 1750
    FLKRTIVRTE NGVRALLDKS SIIRQFYYIK AENTENWTVP PKKIDTSSRG 1800
    QQLYNAGLYA SQHGEEFYTN KIIPLVQRAI EFEGLHIEVP EFHQAVQAYN 1850
    GYFNGTEDQP SQIALASGGT GFGGEVFEN 1879
    Length:1,879
    Mass (Da):209,295
    Last modified:June 6, 2002 - v3
    Checksum:iB03F7FE91FC73F53
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U15301 Genomic RNA. Translation: AAA96501.2.
    M87481 Unassigned DNA. Translation: AAA16216.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U15301 Genomic RNA. Translation: AAA96501.2 .
    M87481 Unassigned DNA. Translation: AAA16216.1 .

    3D structure databases

    ProteinModelPortali P36286.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    Gene3Di 3.40.50.300. 5 hits.
    InterProi IPR003593. AAA+_ATPase.
    IPR016024. ARM-type_fold.
    IPR004004. Helic/Pol/Pept_Calicivir-typ.
    IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR014759. Helicase_SF3_ssRNA_vir.
    IPR027417. P-loop_NTPase.
    IPR000317. Peptidase_C24.
    IPR001205. RNA-dir_pol_C.
    IPR007094. RNA-dir_pol_PSvirus.
    IPR009003. Trypsin-like_Pept_dom.
    [Graphical view ]
    Pfami PF03510. Peptidase_C24. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view ]
    PRINTSi PR00916. 2CENDOPTASE.
    PR00918. CALICVIRUSNS.
    SMARTi SM00382. AAA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48371. SSF48371. 1 hit.
    SSF50494. SSF50494. 1 hit.
    SSF52540. SSF52540. 1 hit.
    PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Neill J.D., Seal B.S., Ridpath J.F.
      Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], SEQUENCE REVISION TO 724-726; 745; 765 AND 774.
    2. "Genetic relatedness of the caliciviruses: San Miguel sea lion and vesicular exanthema of swine viruses constitute a single genotype within the Caliciviridae."
      Neill J.D., Meyer R.F., Seal B.S.
      J. Virol. 69:4484-4488(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 724-1879.
    3. "Nucleotide sequence of the capsid protein gene of two serotypes of San Miguel sea lion virus: identification of conserved and non-conserved amino acid sequences among calicivirus capsid proteins."
      Neill J.D.
      Virus Res. 24:211-222(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1841-1879.

    Entry informationi

    Entry nameiPOLG_SMSV1
    AccessioniPrimary (citable) accession number: P36286
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: June 6, 2002
    Last modified: October 1, 2014
    This is version 94 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3