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Q04544

- POLG_SOUV3

UniProt

Q04544 - POLG_SOUV3

Protein

Genome polyprotein

Gene

ORF1

Organism
Southampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 2 (01 Oct 1996)
      Previous versions | rss
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    Functioni

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

    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.PROSITE-ProRule annotation
    Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei399 – 4002Cleavage; by 3CLproBy similarity
    Sitei762 – 7632Cleavage; by 3CLproBy similarity
    Sitei961 – 9622Cleavage; by 3CLproBy similarity
    Sitei1099 – 11002Cleavage; by 3CLproBy similarity
    Active sitei1129 – 11291For 3CLpro activityPROSITE-ProRule annotation
    Active sitei1153 – 11531For 3CLpro activityPROSITE-ProRule annotation
    Active sitei1238 – 12381For 3CLpro activityPROSITE-ProRule annotation
    Sitei1280 – 12812Cleavage; by 3CLproBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi561 – 5688ATPPROSITE-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

    Host-virus interaction, Viral RNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi3.4.22.66. 5774.

    Protein family/group databases

    MEROPSiC37.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Genome polyprotein
    Cleaved into the following 6 chains:
    Alternative name(s):
    p41
    Alternative name(s):
    VPG
    3C-like protease (EC:3.4.22.66)
    Short name:
    3CLpro
    Alternative name(s):
    Calicivirin
    Gene namesi
    ORF Names:ORF1
    OrganismiSouthampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK)
    Taxonomic identifieri37129 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
    Virus hostiHomo sapiens (Human) [TaxID: 9606]
    ProteomesiUP000007226: Genome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 17881788Genome polyproteinPRO_0000342021Add
    BLAST
    Chaini1 – 399399Protein p48PRO_0000036935Add
    BLAST
    Chaini400 – 762363NTPasePRO_0000036936Add
    BLAST
    Chaini763 – 961199Protein p22PRO_0000036937Add
    BLAST
    Chaini962 – 1099138Viral genome-linked proteinPRO_0000036938Add
    BLAST
    Chaini1100 – 12801813C-like proteasePRO_0000036939Add
    BLAST
    Chaini1281 – 1788508RNA-directed RNA polymerasePRO_0000036940Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei991 – 9911O-(5'-phospho-RNA)-tyrosineBy similarity

    Post-translational modificationi

    Specific enzymatic cleavages in vivo yield mature proteins. 3CLpro is first autocatalytically cleaved, then processes the whole polyprotein.PROSITE-ProRule annotation
    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 p48 interacts with human VAPA.By similarity

    Structurei

    Secondary structure

    1
    1788
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi1102 – 11054
    Beta strandi1108 – 11114
    Beta strandi1114 – 112714
    Helixi1128 – 11303
    Beta strandi1136 – 11383
    Helixi1143 – 11453
    Beta strandi1146 – 11516
    Beta strandi1154 – 11618
    Beta strandi1181 – 11877
    Beta strandi1193 – 120816
    Beta strandi1211 – 122010
    Beta strandi1222 – 12243
    Turni1229 – 12313
    Beta strandi1241 – 12466
    Beta strandi1249 – 125911
    Beta strandi1261 – 12699

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2IPHX-ray1.75A/B1100-1280[»]
    ProteinModelPortaliQ04544.
    SMRiQ04544. Positions 1100-1279, 1285-1785.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ04544.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini533 – 698166SF3 helicasePROSITE-ProRule annotationAdd
    BLAST
    Domaini1100 – 1280181Peptidase C37PROSITE-ProRule annotationAdd
    BLAST
    Domaini1515 – 1636122RdRp catalyticPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi847 – 8504Poly-Gln

    Sequence similaritiesi

    Contains 1 peptidase C37 domain.PROSITE-ProRule annotation
    Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
    Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR000605. 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]
    PfamiPF08405. Calici_PP_N. 1 hit.
    PF05416. Peptidase_C37. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view]
    PRINTSiPR00917. SRSVCYSPTASE.
    SUPFAMiSSF50494. SSF50494. 1 hit.
    SSF52540. SSF52540. 1 hit.
    PROSITEiPS51537. NV_3CL_PRO. 1 hit.
    PS50507. 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.

    Q04544-1 [UniParc]FASTAAdd to Basket

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    MMMASKDVVA TNVASNNNAN NTSATSRFLS RFKGLGGGAS PPSPIKIKST     50
    EMALGLIGRT TPEPTGTAGP PPKQQRDRPP RTQEEVQYGM GWSDRPIDQN 100
    VKSWEELDTT VKEEILDNHK EWFDAGGLGP CTMPPTYERV KDDSPPGEQV 150
    KWSARDGVNI GVERLTTVSG PEWNLCPLPP IDLRNMEPAS EPTIGDMIEF 200
    YEGHIYHYSI YIGQGKTVGV HSPQAAFSVA RVTIQPIAAW WRVCYIPQPK 250
    HRLSYDQLKE LENEPWPYAA ITNNCFEFCC QVMNLEDTWL QRRLVTSGRF 300
    HHPTQSWSQQ TPEFQQDSKL ELVRDAILAA VNGLVSQPFK NFLGKLKPLN 350
    VLNILSNCDW TFMGVVEMVI LLLELFGVFW NPPDVSNFIA SLLPDFHLQG 400
    PEDLARDLVP VILGGIGLAI GFTRDKVTKV MKSAVDGLRA ATQLGQYGLE 450
    IFSLLKKYFF GGDQTERTLK GIEAAVIDME VLSSTSVTQL VRDKQAAKAY 500
    MNILDNEEEK ARKLSAKNAD PHVISSTNAL ISRISMARSA LAKAQAEMTS 550
    RMRPVVIMMC GPPGIGKTKA AEHLAKRLAN EIRPGGKVGL VPREAVDHWD 600
    GYHGEEVMLW DDYGMTKILD DCNKLQAIAD SAPLTLNCDR IENKGMQFVS 650
    DAIVITTNAP GPAPVDFVNL GPVCRRVDFL VYCSAPEVEQ IRRVSPGDTS 700
    ALKDCFKLDF SHLKMELAPQ GGFDNQGNTP FGKGTMKPTT INRLLIQAVA 750
    LTMERQDEFQ LQGKMYDFDD DRVSAFTTMA RDNGLGILSM AGLGKKLRGV 800
    TTMEGLKNAL KGYKISACTI KWQAKVYSLE SDGNSVNIKE ERNILTQQQQ 850
    SVCTASVALT RLRAARAVAY ASCIQSAITS ILQIAGSALV VNRAVKRMFG 900
    TRTATLSLEG PPREHKCRVH MAKAAGKGPI GHDDVVEKYG LCETEEDEEV 950
    AHTEIPSATM EGKNKGKNKK GRGRRNNYNA FSRRGLNDEE YEEYKKIREE 1000
    KGGNYSIQEY LEDRQRYEEE LAEVQAGGDG GIGETEMEIR HRVFYKSKSR 1050
    KHHQEERRQL GLVTGSDIRK RKPIDWTPPK SAWADDEREV DYNEKISFEA 1100
    PPTLWSRVTK FGSGWGFWVS PTVFITTTHV IPTSAKEFFG EPLTSIAIHR 1150
    AGEFTLFRFS KKIRPDLTGM ILEEGCPEGT VCSVLIKRDS GELLPLAVRM 1200
    GAIASMRIQG RLVHGQSGML LTGANAKGMD LGTIPGDCGA PYVYKRANDW 1250
    VVCGVHAAAT KSGNTVVCAV QASEGETTLE GGDKGHYAGH EIIKHGCGPA 1300
    LSTKTKFWKS SPEPLPPGVY EPAYLGGRDP RVTVGPSLQQ VLRDQLKPFA 1350
    EPRGRMPEPG LLEAAVETVT SSLEQVMDTP VPWSYSDACQ SLDKTTSSGF 1400
    PYHRRKNDDW NGTTFVRELG EQAAHANNMY EQAKSMKPMY TGALKDELVK 1450
    PEKVYQKVKK RLLWGADLGT VVRAARAFGP FCDAIKSHTI KLPIKVGMNS 1500
    IEDGPLIYAE HSKYKYHFDA DYTAWDSTQN RQIMTESFSI MCRLTASPEL 1550
    ASVVAQDLLA PSEMDVGDYV IRVKEGLPSG FPCTSQVNSI NHWLITLCAL 1600
    SEVTGLSPDV IQSMSYFSFY GDDEIVSTDI EFDPAKLTQV LREYGLRPTR 1650
    PDKSEGPIIV RKSVDGLVFL RRTISRDAAG FQGRLDRASI ERQIYWTRGP 1700
    NHSDPFETLV PHQQRKVQLI SLLGEASLHG EKFYRKISSK VIQEIKTGGL 1750
    EMYVPGWQAM FRWMRFHDLG LWTGDRNLLP EFVNDDGV 1788
    Length:1,788
    Mass (Da):198,582
    Last modified:October 1, 1996 - v2
    Checksum:i9ED4F6529793652F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L07418 Genomic RNA. Translation: AAA92983.1.
    PIRiA37491.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L07418 Genomic RNA. Translation: AAA92983.1 .
    PIRi A37491.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2IPH X-ray 1.75 A/B 1100-1280 [» ]
    ProteinModelPortali Q04544.
    SMRi Q04544. Positions 1100-1279, 1285-1785.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi C37.001.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    BRENDAi 3.4.22.66. 5774.

    Miscellaneous databases

    EvolutionaryTracei Q04544.

    Family and domain databases

    Gene3Di 3.40.50.300. 2 hits.
    InterProi IPR000605. 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 ]
    Pfami PF08405. Calici_PP_N. 1 hit.
    PF05416. Peptidase_C37. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view ]
    PRINTSi PR00917. SRSVCYSPTASE.
    SUPFAMi SSF50494. SSF50494. 1 hit.
    SSF52540. SSF52540. 1 hit.
    PROSITEi PS51537. NV_3CL_PRO. 1 hit.
    PS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiPOLG_SOUV3
    AccessioniPrimary (citable) accession number: Q04544
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 94 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3