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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).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
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)-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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        10         20         30         40         50
MMMASKDVVA TNVASNNNAN NTSATSRFLS RFKGLGGGAS PPSPIKIKST
60 70 80 90 100
EMALGLIGRT TPEPTGTAGP PPKQQRDRPP RTQEEVQYGM GWSDRPIDQN
110 120 130 140 150
VKSWEELDTT VKEEILDNHK EWFDAGGLGP CTMPPTYERV KDDSPPGEQV
160 170 180 190 200
KWSARDGVNI GVERLTTVSG PEWNLCPLPP IDLRNMEPAS EPTIGDMIEF
210 220 230 240 250
YEGHIYHYSI YIGQGKTVGV HSPQAAFSVA RVTIQPIAAW WRVCYIPQPK
260 270 280 290 300
HRLSYDQLKE LENEPWPYAA ITNNCFEFCC QVMNLEDTWL QRRLVTSGRF
310 320 330 340 350
HHPTQSWSQQ TPEFQQDSKL ELVRDAILAA VNGLVSQPFK NFLGKLKPLN
360 370 380 390 400
VLNILSNCDW TFMGVVEMVI LLLELFGVFW NPPDVSNFIA SLLPDFHLQG
410 420 430 440 450
PEDLARDLVP VILGGIGLAI GFTRDKVTKV MKSAVDGLRA ATQLGQYGLE
460 470 480 490 500
IFSLLKKYFF GGDQTERTLK GIEAAVIDME VLSSTSVTQL VRDKQAAKAY
510 520 530 540 550
MNILDNEEEK ARKLSAKNAD PHVISSTNAL ISRISMARSA LAKAQAEMTS
560 570 580 590 600
RMRPVVIMMC GPPGIGKTKA AEHLAKRLAN EIRPGGKVGL VPREAVDHWD
610 620 630 640 650
GYHGEEVMLW DDYGMTKILD DCNKLQAIAD SAPLTLNCDR IENKGMQFVS
660 670 680 690 700
DAIVITTNAP GPAPVDFVNL GPVCRRVDFL VYCSAPEVEQ IRRVSPGDTS
710 720 730 740 750
ALKDCFKLDF SHLKMELAPQ GGFDNQGNTP FGKGTMKPTT INRLLIQAVA
760 770 780 790 800
LTMERQDEFQ LQGKMYDFDD DRVSAFTTMA RDNGLGILSM AGLGKKLRGV
810 820 830 840 850
TTMEGLKNAL KGYKISACTI KWQAKVYSLE SDGNSVNIKE ERNILTQQQQ
860 870 880 890 900
SVCTASVALT RLRAARAVAY ASCIQSAITS ILQIAGSALV VNRAVKRMFG
910 920 930 940 950
TRTATLSLEG PPREHKCRVH MAKAAGKGPI GHDDVVEKYG LCETEEDEEV
960 970 980 990 1000
AHTEIPSATM EGKNKGKNKK GRGRRNNYNA FSRRGLNDEE YEEYKKIREE
1010 1020 1030 1040 1050
KGGNYSIQEY LEDRQRYEEE LAEVQAGGDG GIGETEMEIR HRVFYKSKSR
1060 1070 1080 1090 1100
KHHQEERRQL GLVTGSDIRK RKPIDWTPPK SAWADDEREV DYNEKISFEA
1110 1120 1130 1140 1150
PPTLWSRVTK FGSGWGFWVS PTVFITTTHV IPTSAKEFFG EPLTSIAIHR
1160 1170 1180 1190 1200
AGEFTLFRFS KKIRPDLTGM ILEEGCPEGT VCSVLIKRDS GELLPLAVRM
1210 1220 1230 1240 1250
GAIASMRIQG RLVHGQSGML LTGANAKGMD LGTIPGDCGA PYVYKRANDW
1260 1270 1280 1290 1300
VVCGVHAAAT KSGNTVVCAV QASEGETTLE GGDKGHYAGH EIIKHGCGPA
1310 1320 1330 1340 1350
LSTKTKFWKS SPEPLPPGVY EPAYLGGRDP RVTVGPSLQQ VLRDQLKPFA
1360 1370 1380 1390 1400
EPRGRMPEPG LLEAAVETVT SSLEQVMDTP VPWSYSDACQ SLDKTTSSGF
1410 1420 1430 1440 1450
PYHRRKNDDW NGTTFVRELG EQAAHANNMY EQAKSMKPMY TGALKDELVK
1460 1470 1480 1490 1500
PEKVYQKVKK RLLWGADLGT VVRAARAFGP FCDAIKSHTI KLPIKVGMNS
1510 1520 1530 1540 1550
IEDGPLIYAE HSKYKYHFDA DYTAWDSTQN RQIMTESFSI MCRLTASPEL
1560 1570 1580 1590 1600
ASVVAQDLLA PSEMDVGDYV IRVKEGLPSG FPCTSQVNSI NHWLITLCAL
1610 1620 1630 1640 1650
SEVTGLSPDV IQSMSYFSFY GDDEIVSTDI EFDPAKLTQV LREYGLRPTR
1660 1670 1680 1690 1700
PDKSEGPIIV RKSVDGLVFL RRTISRDAAG FQGRLDRASI ERQIYWTRGP
1710 1720 1730 1740 1750
NHSDPFETLV PHQQRKVQLI SLLGEASLHG EKFYRKISSK VIQEIKTGGL
1760 1770 1780
EMYVPGWQAM FRWMRFHDLG LWTGDRNLLP EFVNDDGV
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