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P36286

- POLG_SMSV1

UniProt

P36286 - POLG_SMSV1

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Protein

Genome polyprotein

Gene
ORF1
Organism
San Miguel sea lion virus serotype 1 (SMSV-1) (SMSV serotype 1)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

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 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.

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).

Sites

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi590 – 5978ATP Reviewed prediction

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
Complete GO annotation...

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 p32 By similarityPRO_0000036928Add
BLAST
Chaini436 – 791356NTPase By similarityPRO_0000036929Add
BLAST
Chaini792 – 1070279Protein p30 By similarityPRO_0000036930Add
BLAST
Chaini1071 – 1183113Viral genome-linked protein By similarityPRO_0000036931Add
BLAST
Chaini1184 – 1879696Protease-polymerase p76 By similarityPRO_0000036932Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1093 – 10931O-(5'-phospho-RNA)-tyrosine By 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.
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.

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.

Structurei

3D structure databases

ProteinModelPortaliP36286.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini564 – 720157SF3 helicaseAdd
BLAST
Domaini1207 – 1311105Peptidase C24Add
BLAST
Domaini1591 – 1716126RdRp catalyticAdd
BLAST

Domaini

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

Sequence similaritiesi

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: May 14, 2014
This is version 93 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

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