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P36286 (POLG_SMSV1) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 92. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 6 chains:

  1. Protein p16
  2. Protein p32
  3. NTPase
    EC=3.6.1.15
    Alternative name(s):
    p39
  4. Protein p30
  5. Viral genome-linked protein
    Alternative name(s):
    VPg
    p13
  6. Protease-polymerase p76
    Short name=Pro-Pol
    EC=2.7.7.48
    EC=3.4.22.66
Gene names
ORF Names:ORF1
OrganismSan Miguel sea lion virus serotype 1 (SMSV-1) (SMSV serotype 1) [Complete proteome]
Taxonomic identifier36406 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostOtariidae (fur seals & sea lions) [TaxID: 9702]

Protein attributes

Sequence length1879 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 activity

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).

Subunit structure

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.

Domain

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

Post-translational modification

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.

Sequence similarities

Contains 1 peptidase C24 domain.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 18791879Genome polyprotein
PRO_0000342015
Chain1 – 148148Protein p16
PRO_0000342016
Chain149 – 435287Protein p32 By similarity
PRO_0000036928
Chain436 – 791356NTPase By similarity
PRO_0000036929
Chain792 – 1070279Protein p30 By similarity
PRO_0000036930
Chain1071 – 1183113Viral genome-linked protein By similarity
PRO_0000036931
Chain1184 – 1879696Protease-polymerase p76 By similarity
PRO_0000036932

Regions

Domain564 – 720157SF3 helicase
Domain1207 – 1311105Peptidase C24
Domain1591 – 1716126RdRp catalytic
Nucleotide binding590 – 5978ATP Potential

Sites

Active site12221For protease activity By similarity
Active site12431For protease activity By similarity
Active site13051For protease activity By similarity
Site148 – 1492Cleavage; by Pro-Pol By similarity
Site435 – 4362Cleavage; by Pro-Pol By similarity
Site791 – 7922Cleavage; by Pro-Pol By similarity
Site1070 – 10712Cleavage; by Pro-Pol By similarity
Site1183 – 11842Cleavage; by Pro-Pol By similarity

Amino acid modifications

Modified residue10931O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

Sequence LengthMass (Da)Tools
P36286 [UniParc].

Last modified June 6, 2002. Version 3.
Checksum: B03F7FE91FC73F53

FASTA1,879209,295
        10         20         30         40         50         60 
MAQTLSKISN KENASVGLWP KRFKPHQPTP TWMVRCGPLD HDSRHGRDPV RASPQAKRVR 

        70         80         90        100        110        120 
TPNPYPRHLK PAASAVVRSG TNPSHLKPTS TDVVRSGPET PCCEAKDGGV VRSCKTCNLK 

       130        140        150        160        170        180 
PAHDSKAVSF FPAQTDGLTG DEPEFIAEAC PSCVLYDTCP NCTSRAINDD GSTDGTIPSW 

       190        200        210        220        230        240 
DQIETTPAFL SLLSNTDEEM SADELTNLAA HLRKAFETGS HPPNVDYSKD QLQGLLEMAE 

       250        260        270        280        290        300 
AALPPARRQT LPFYQQRLEA RRTWREKIFN LPLDELSKIL TTSKDRFQRC AAWKVVLEKA 

       310        320        330        340        350        360 
VLAKEYGEEA YAYAQEALKN INSFDVNLVL KMAAGTFIGH LRMMTVDNPD MVSYLPKLIV 

       370        380        390        400        410        420 
KLKPLTLKMI IDNHENTKEG WLVTLTSLAE LYGMVEVAID FVPTVIGNLF DLLMKTTSKV 

       430        440        450        460        470        480 
YSMFKSVILA TFTSESLDFT NPFWYAIAAI LCFLITGAIP HNGKMKIIKN ILSNATGIVA 

       490        500        510        520        530        540 
GVKAIQTLGA MFSTWSNERL VNDLSSRTIA ITELNNPTIT ADIDAVINLQ RLAETLREEV 

       550        560        570        580        590        600 
KSHTLNPLMQ PYTPILRNLM SALDNVISCC TRRKAIATKR TAPVAVILTG PPGCGKTTAA 

       610        620        630        640        650        660 
FALAKRLSQQ KPSIISLDVD HHDTYTGNEV CIIDEFDSSD KVDYANFVVN MVNTNPMVLN 

       670        680        690        700        710        720 
CDLVENKGKT FRSKYVIMKS NSETPVKPTS RRAGAFYRRV MIVDVKNTAV ENWKRENPGK 

       730        740        750        760        770        780 
PVPKWCFNKD FSHLHLSMRG TEAYWREYVL DPTGRNHQSQ KAPPDQHVTL EQLDQKMVVQ 

       790        800        810        820        830        840 
HTTNTSEFVT QAGEVPVFGF VCQNNEIDTV YNLLAAVKAR YGANFNLYKG MTRTAHENSG 

       850        860        870        880        890        900 
CGAHVHVISR EDNFRGKAFT VNRSRLESVP HLEGDSFRRS LGVVMSDKDV TTMFYYIKGK 

       910        920        930        940        950        960 
VINDQVNLTE LPANQHVVTV HTVYDMAWAL RRHLKWTGQW QLIKAAYEIM CYPDTAACAL 

       970        980        990       1000       1010       1020 
RNWMDSTDFS EEHVVTQFIA PGGTIILESC YGARMWATGQ RLIRAGGLTE AGGPQGGVRF 

      1030       1040       1050       1060       1070       1080 
AGLGARNVPW SEILREFMTL ISHIWSQIKG ATVVLTALTF YLKRFRPRVE AKGKNKNKGP 

      1090       1100       1110       1120       1130       1140 
RKNTGVALTD DEYDEWRQYK AEKKLDLTVE DFLQLRHRAA MGADDTDAVK FRCWYSERQR 

      1150       1160       1170       1180       1190       1200 
NYHDLEDVTI IGRGGVKREL IRKGPLRPRG NDFYDEPDDW YSEGVIDGVT HKNAIVSVDD 

      1210       1220       1230       1240       1250       1260 
VDGMHKGYAL HIGHGVYMSL KHVVSGNAKI LSEEPKNLTF NGELATFRLN TTLPTAAPVG 

      1270       1280       1290       1300       1310       1320 
TSKPIKDPWG NPVSTDWQFK NYNTTSGNIY GACGSSCSLT RQGDCGLPYV DDHGVVVGLH 

      1330       1340       1350       1360       1370       1380 
AGSGGDKCPS RKLIVPYVKV DMRIRDTCTK EYYKDNVPMI SYKGLLVKET GEPRTIMKGT 

      1390       1400       1410       1420       1430       1440 
RLHVSPAHTD DYEECTHQPA SLGAGDPRCP MSLTGIMVNN LQPYTEAPRT DTATLNRVTK 

      1450       1460       1470       1480       1490       1500 
MLISHMEGYV PKIHKTEEDM ISAFYMLNHD TSCGPYIGGR KKDHVKDGVL DKNLLDLLSS 

      1510       1520       1530       1540       1550       1560 
KWNRAKCGLA LPHEYALGLK DELRPKDKVA VGKRRLIWGC DVGVSTVCRA AFKRVSESIM 

      1570       1580       1590       1600       1610       1620 
ANHALGFIQV GINMDGPAVE DPFKRLERPK HDRYCVDYSK WDSTQPPKVT SQSIDILRHF 

      1630       1640       1650       1660       1670       1680 
TDKSPIVDSA CATLKSNPIG IFNGVAFKVA GGLPSGMPLT SIINSLNHCL MVGSAVVKAL 

      1690       1700       1710       1720       1730       1740 
EDSGVQVTWN IFDSMDLFTY GDDGVYIVPP LISSVMPKVF SNLRQFGLKP TRTDKTDAEI 

      1750       1760       1770       1780       1790       1800 
TPIPADEPVE FLKRTIVRTE NGVRALLDKS SIIRQFYYIK AENTENWTVP PKKIDTSSRG 

      1810       1820       1830       1840       1850       1860 
QQLYNAGLYA SQHGEEFYTN KIIPLVQRAI EFEGLHIEVP EFHQAVQAYN GYFNGTEDQP 

      1870 
SQIALASGGT GFGGEVFEN 

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U15301 Genomic RNA. Translation: AAA96501.2.
M87481 Unassigned DNA. Translation: AAA16216.1.

3D structure databases

ProteinModelPortalP36286.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.40.50.300. 5 hits.
InterProIPR003593. 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]
PfamPF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMSSF48371. SSF48371. 1 hit.
SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLG_SMSV1
AccessionPrimary (citable) accession number: P36286
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 6, 2002
Last modified: April 16, 2014
This is version 92 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries