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Q04544

- POLG_SOUV3

UniProt

Q04544 - POLG_SOUV3

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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

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.
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 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
Sitei399 – 4002Cleavage; by 3CLpro By similarity
Sitei762 – 7632Cleavage; by 3CLpro By similarity
Sitei961 – 9622Cleavage; by 3CLpro By similarity
Sitei1099 – 11002Cleavage; by 3CLpro By similarity
Active sitei1129 – 11291For 3CLpro activity By similarity
Active sitei1153 – 11531For 3CLpro activity By similarity
Active sitei1238 – 12381For 3CLpro activity By similarity
Sitei1280 – 12812Cleavage; by 3CLpro By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi561 – 5688ATP By similarity

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

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)-tyrosine By similarity

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. 3CLpro is first autocatalytically cleaved, then processes the whole polyprotein By similarity.1 Publication
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 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.

Miscellaneous databases

EvolutionaryTraceiQ04544.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini533 – 698166SF3 helicaseAdd
BLAST
Domaini1100 – 1280181Peptidase C37Add
BLAST
Domaini1515 – 1636122RdRp catalyticAdd
BLAST

Compositional bias

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

Sequence similaritiesi

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: May 14, 2014
This is version 93 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

Similar proteinsi