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Q04544 (POLG_SOUV3) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 6 chains:

  1. Protein p48
  2. NTPase
    EC=3.6.1.15
    Alternative name(s):
    p41
  3. Protein p22
  4. Viral genome-linked protein
    Alternative name(s):
    VPG
  5. 3C-like protease
    Short name=3CLpro
    EC=3.4.22.66
    Alternative name(s):
    Calicivirin
  6. RNA-directed RNA polymerase
    Short name=RdRp
    EC=2.7.7.48
Gene names
ORF Names:ORF1
OrganismSouthampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK) [Complete proteome]
Taxonomic identifier37129 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length1788 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Protein p48 may play a role in viral replication by interacting with host VAPA, a vesicle-associated membrane protein that plays a role in SNARE-mediated vesicle fusion. This interaction may target replication complex to intracellular membranes By similarity.

NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity By similarity.

Protein P22 may play a role in targeting replication complex to intracellular membranes 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.

3C-like protease processes the polyprotein: 3CLpro-RdRp is first released by autocleavage, then all other proteins are cleaved. May cleave polyadenylate-binding protein thereby inhibiting cellular translation By similarity.

RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications 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 p48 interacts with human VAPA By similarity.

Post-translational modification

Specific enzymatic cleavages in vivo yield mature proteins. 3CLpro is first autocatalytically cleaved, then processes the whole polyprotein By similarity. Ref.3

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 C37 domain.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 17881788Genome polyprotein
PRO_0000342021
Chain1 – 399399Protein p48
PRO_0000036935
Chain400 – 762363NTPase
PRO_0000036936
Chain763 – 961199Protein p22
PRO_0000036937
Chain962 – 1099138Viral genome-linked protein
PRO_0000036938
Chain1100 – 12801813C-like protease
PRO_0000036939
Chain1281 – 1788508RNA-directed RNA polymerase
PRO_0000036940

Regions

Domain533 – 698166SF3 helicase
Domain1100 – 1280181Peptidase C37
Domain1515 – 1636122RdRp catalytic
Nucleotide binding561 – 5688ATP By similarity
Compositional bias847 – 8504Poly-Gln

Sites

Active site11291For 3CLpro activity By similarity
Active site11531For 3CLpro activity By similarity
Active site12381For 3CLpro activity By similarity
Site399 – 4002Cleavage; by 3CLpro By similarity
Site762 – 7632Cleavage; by 3CLpro By similarity
Site961 – 9622Cleavage; by 3CLpro By similarity
Site1099 – 11002Cleavage; by 3CLpro By similarity
Site1280 – 12812Cleavage; by 3CLpro By similarity

Amino acid modifications

Modified residue9911O-(5'-phospho-RNA)-tyrosine By similarity

Secondary structure

............................... 1788
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q04544 [UniParc].

Last modified October 1, 1996. Version 2.
Checksum: 9ED4F6529793652F

FASTA1,788198,582
        10         20         30         40         50         60 
MMMASKDVVA TNVASNNNAN NTSATSRFLS RFKGLGGGAS PPSPIKIKST EMALGLIGRT 

        70         80         90        100        110        120 
TPEPTGTAGP PPKQQRDRPP RTQEEVQYGM GWSDRPIDQN VKSWEELDTT VKEEILDNHK 

       130        140        150        160        170        180 
EWFDAGGLGP CTMPPTYERV KDDSPPGEQV KWSARDGVNI GVERLTTVSG PEWNLCPLPP 

       190        200        210        220        230        240 
IDLRNMEPAS EPTIGDMIEF YEGHIYHYSI YIGQGKTVGV HSPQAAFSVA RVTIQPIAAW 

       250        260        270        280        290        300 
WRVCYIPQPK HRLSYDQLKE LENEPWPYAA ITNNCFEFCC QVMNLEDTWL QRRLVTSGRF 

       310        320        330        340        350        360 
HHPTQSWSQQ TPEFQQDSKL ELVRDAILAA VNGLVSQPFK NFLGKLKPLN VLNILSNCDW 

       370        380        390        400        410        420 
TFMGVVEMVI LLLELFGVFW NPPDVSNFIA SLLPDFHLQG PEDLARDLVP VILGGIGLAI 

       430        440        450        460        470        480 
GFTRDKVTKV MKSAVDGLRA ATQLGQYGLE IFSLLKKYFF GGDQTERTLK GIEAAVIDME 

       490        500        510        520        530        540 
VLSSTSVTQL VRDKQAAKAY MNILDNEEEK ARKLSAKNAD PHVISSTNAL ISRISMARSA 

       550        560        570        580        590        600 
LAKAQAEMTS RMRPVVIMMC GPPGIGKTKA AEHLAKRLAN EIRPGGKVGL VPREAVDHWD 

       610        620        630        640        650        660 
GYHGEEVMLW DDYGMTKILD DCNKLQAIAD SAPLTLNCDR IENKGMQFVS DAIVITTNAP 

       670        680        690        700        710        720 
GPAPVDFVNL GPVCRRVDFL VYCSAPEVEQ IRRVSPGDTS ALKDCFKLDF SHLKMELAPQ 

       730        740        750        760        770        780 
GGFDNQGNTP FGKGTMKPTT INRLLIQAVA LTMERQDEFQ LQGKMYDFDD DRVSAFTTMA 

       790        800        810        820        830        840 
RDNGLGILSM AGLGKKLRGV TTMEGLKNAL KGYKISACTI KWQAKVYSLE SDGNSVNIKE 

       850        860        870        880        890        900 
ERNILTQQQQ SVCTASVALT RLRAARAVAY ASCIQSAITS ILQIAGSALV VNRAVKRMFG 

       910        920        930        940        950        960 
TRTATLSLEG PPREHKCRVH MAKAAGKGPI GHDDVVEKYG LCETEEDEEV AHTEIPSATM 

       970        980        990       1000       1010       1020 
EGKNKGKNKK GRGRRNNYNA FSRRGLNDEE YEEYKKIREE KGGNYSIQEY LEDRQRYEEE 

      1030       1040       1050       1060       1070       1080 
LAEVQAGGDG GIGETEMEIR HRVFYKSKSR KHHQEERRQL GLVTGSDIRK RKPIDWTPPK 

      1090       1100       1110       1120       1130       1140 
SAWADDEREV DYNEKISFEA PPTLWSRVTK FGSGWGFWVS PTVFITTTHV IPTSAKEFFG 

      1150       1160       1170       1180       1190       1200 
EPLTSIAIHR AGEFTLFRFS KKIRPDLTGM ILEEGCPEGT VCSVLIKRDS GELLPLAVRM 

      1210       1220       1230       1240       1250       1260 
GAIASMRIQG RLVHGQSGML LTGANAKGMD LGTIPGDCGA PYVYKRANDW VVCGVHAAAT 

      1270       1280       1290       1300       1310       1320 
KSGNTVVCAV QASEGETTLE GGDKGHYAGH EIIKHGCGPA LSTKTKFWKS SPEPLPPGVY 

      1330       1340       1350       1360       1370       1380 
EPAYLGGRDP RVTVGPSLQQ VLRDQLKPFA EPRGRMPEPG LLEAAVETVT SSLEQVMDTP 

      1390       1400       1410       1420       1430       1440 
VPWSYSDACQ SLDKTTSSGF PYHRRKNDDW NGTTFVRELG EQAAHANNMY EQAKSMKPMY 

      1450       1460       1470       1480       1490       1500 
TGALKDELVK PEKVYQKVKK RLLWGADLGT VVRAARAFGP FCDAIKSHTI KLPIKVGMNS 

      1510       1520       1530       1540       1550       1560 
IEDGPLIYAE HSKYKYHFDA DYTAWDSTQN RQIMTESFSI MCRLTASPEL ASVVAQDLLA 

      1570       1580       1590       1600       1610       1620 
PSEMDVGDYV IRVKEGLPSG FPCTSQVNSI NHWLITLCAL SEVTGLSPDV IQSMSYFSFY 

      1630       1640       1650       1660       1670       1680 
GDDEIVSTDI EFDPAKLTQV LREYGLRPTR PDKSEGPIIV RKSVDGLVFL RRTISRDAAG 

      1690       1700       1710       1720       1730       1740 
FQGRLDRASI ERQIYWTRGP NHSDPFETLV PHQQRKVQLI SLLGEASLHG EKFYRKISSK 

      1750       1760       1770       1780 
VIQEIKTGGL EMYVPGWQAM FRWMRFHDLG LWTGDRNLLP EFVNDDGV 

« Hide

References

[1]"Sequence and genome organization of a human small round-structured (Norwalk-like) virus."
Lambden P.R., Caul E.O., Ashley C.R., Clarke I.N.
Science 259:516-519(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"A conserved sequence motif at the 5' terminus of the Southampton virus genome is characteristic of the Caliciviridae."
Lambden P.R., Liu B., Clarke I.N.
Virus Genes 10:149-152(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION.
[3]"Identification of further proteolytic cleavage sites in the Southampton calicivirus polyprotein by expression of the viral protease in E. coli."
Liu B.L., Viljoen G.J., Clarke I.N., Lambden P.R.
J. Gen. Virol. 80:291-296(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L07418 Genomic RNA. Translation: AAA92983.1.
PIRA37491.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2IPHX-ray1.75A/B1100-1280[»]
ProteinModelPortalQ04544.
SMRQ04544. Positions 1100-1279, 1285-1785.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSC37.001.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BRENDA3.4.22.66. 5774.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR001665. Norovirus_pept_C37.
IPR027417. P-loop_NTPase.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
IPR013614. Viral_PP_Calicivir_N.
[Graphical view]
PfamPF08405. Calici_PP_N. 1 hit.
PF05416. Peptidase_C37. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSPR00917. SRSVCYSPTASE.
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEPS51537. NV_3CL_PRO. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ04544.

Entry information

Entry namePOLG_SOUV3
AccessionPrimary (citable) accession number: Q04544
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1996
Last modified: May 14, 2014
This is version 93 of the entry and version 2 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references