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Protein

Genome polyprotein

Gene

ORF1

Organism
Feline calicivirus (strain Japanese F4) (FCV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity (By similarity).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
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, eIF4G2 and PABP1 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).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).PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei1110For protease activity1 Publication1
Active sitei1131For protease activity1 Publication1
Active sitei1193For protease activity1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi484 – 491ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Protein family/group databases

MEROPSiC24.002.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 6 chains:
Alternative name(s):
p39
Alternative name(s):
VPg
p13
Protease-polymerase p76 (EC:2.7.7.48, EC:3.4.22.66)
Short name:
Pro-Pol
Gene namesi
ORF Names:ORF1
OrganismiFeline calicivirus (strain Japanese F4) (FCV)
Taxonomic identifieri11980 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostiFelidae (cat family) [TaxID: 9681]
Proteomesi
  • UP000008668 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1079H → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1093H → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1099H → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1102H → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1110H → A: Complete loss of protease activity in vitro. 1 Publication1
Mutagenesisi1121E → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1125D → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1131E → A: Complete loss of protease activity in vitro. 1 Publication1
Mutagenesisi1155D → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1164E → A: No effect on protease activity in vitro. 1 Publication1
Mutagenesisi1193C → A: Complete loss of protease activity in vitro. 1 Publication1
Mutagenesisi1208H → A: Complete loss of protease activity in vitro. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003419911 – 1763Genome polyproteinAdd BLAST1763
ChainiPRO_00003419921 – 46Protein p5.6Add BLAST46
ChainiPRO_000034199347 – 331Protein p32Add BLAST285
ChainiPRO_0000341994332 – 685NTPaseAdd BLAST354
ChainiPRO_0000341995686 – 960Protein p30Add BLAST275
ChainiPRO_0000341996961 – 1071Viral genome-linked proteinAdd BLAST111
ChainiPRO_00000368991072 – 1763Protease-polymerase p76Add BLAST692

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei984O-(5'-phospho-RNA)-tyrosineBy similarity1

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. Pro-Pol is first autocatalytically cleaved, then processes the whole polyprotein.
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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei46 – 47Cleavage; by Pro-PolBy similarity2
Sitei331 – 332Cleavage; by Pro-PolBy similarity2
Sitei685 – 686Cleavage; by Pro-PolBy similarity2
Sitei960 – 961Cleavage; by Pro-PolBy similarity2
Sitei1071 – 1072Cleavage; by Pro-PolBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

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).By similarity

Structurei

3D structure databases

ProteinModelPortaliP27408.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini458 – 614SF3 helicasePROSITE-ProRule annotationAdd BLAST157
Domaini1095 – 1199Peptidase C24Add BLAST105
Domaini1478 – 1603RdRp catalyticPROSITE-ProRule annotationAdd BLAST126

Domaini

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

Sequence similaritiesi

Contains 1 peptidase C24 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.300. 4 hits.
InterProiIPR003593. AAA+_ATPase.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR009003. Peptidase_S1_PA.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[Graphical view]
PfamiPF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 4 hits.
PROSITEiPS50507. 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.

P27408-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQTLSFVLK THSVRKDFVH SVKVTLARRR DLQYLYNKLA RTMRAEACPS
60 70 80 90 100
CSSYDVCPNC TSSDIPDNGS STTSIPSWED VTKTSTYSLL LSEDTSDELC
110 120 130 140 150
PDDLVNVAAH IRKALSTQAH PANTEMCKEQ LTSLLVMAEA MLPQRSRASI
160 170 180 190 200
PLHQQHQAAR LEWREKFFSK PLDFLLERIG VSKDILQITA IWKIILEKAC
210 220 230 240 250
YCKSYGEQWF CAAKQKLREM RTFESDTLKP LVGAFIDGLR FMTVDNPNPM
260 270 280 290 300
GFLPKLIGLV KPLNLAMIID NHENTLSGWV VTLTAIMELY NITECTIDVI
310 320 330 340 350
TSLVTGFYDK ISKATKFFSQ VKALFTGFRS EDVANSFWYM AAAILCYLIT
360 370 380 390 400
GLIPNNGRFS KIKACLSGAT TLVSGIIATQ KLAAMFATWN SESIVNELSA
410 420 430 440 450
RTVAISELNN PTTTSDTDSV ERLLELAKIL HEEIKVHTLN PIMQSYNPIL
460 470 480 490 500
RNLMSTLDGV ITSCNKRKAI ARKRQVPVCY ILTGPPGCGK TTAAQALAKK
510 520 530 540 550
LSDQEPSVIN LDVDHHDTYT GNEVCIIDEF DSSDKVDYAN FVIGMVNSAP
560 570 580 590 600
MVLNCDMLEN KGKLFTSKYI IMTSNSETPV KPSSKRAGAF YRRVTIIDVT
610 620 630 640 650
NPLVESHKRA RPGTSVPRSC YKKNFSHLSL AKRGAECWCK EYVLDPKGLQ
660 670 680 690 700
HQTIKAPPPT FLNIDSLAQT MKQDFVLKNM AFEAEDGCSE HRYGFICQQS
710 720 730 740 750
EVETVRRLLN AIRARLNATF TVCVGPEASH SIGCTAHVLT PDEPFNGRRF
760 770 780 790 800
IVSRCNEASL AALEGNCVQS ALGVCMSNKD LTHLCHFIRG KIVNDSVRLD
810 820 830 840 850
ELPANQHVVT VNSVFDLAWA LRRHLTLTGQ FQAIRAAYDV LTVPDKVPAM
860 870 880 890 900
LRHWMDETSF SDEHVVTQFV TPGGVVILES CGGARIWALG HNVIRAGGVT
910 920 930 940 950
ATPTGGCVRL VGLSAQTLPW SEIFRELFTL LGRIWSSIKV STLVLTALGM
960 970 980 990 1000
YASRFRPKSE AKGKTKSKIG PYRGRGVALT DDEYDEWREH NANRKLDLSV
1010 1020 1030 1040 1050
EDFLMLRHRA ALGADDADAV KFRSWWNSRT RPGDGFEDVT VIGKGGVKHE
1060 1070 1080 1090 1100
KIRTSTLRAV DRGYDVSFAE ESGPGTKFHK NAIGSVTDVC GEHKGYCVHM
1110 1120 1130 1140 1150
GHGVYASVAH VVKGDSYFLG ERIFDVKTNG EFCCFRSTKI LPSAAPFFSG
1160 1170 1180 1190 1200
KPTRDPWGSP VATEWKPKAY TTTSGKIVGC FATTSTETHP GDCGLPYIDD
1210 1220 1230 1240 1250
NGRVTGLHTG SGGPKTPSAK LVVPYIHIDM KNKSVTPQKY DETKPNISYK
1260 1270 1280 1290 1300
GLVCKQLDEI RIIPKGTRLH VSPAHVDDFE ECSHQPASLG SGDPRCPKSL
1310 1320 1330 1340 1350
TAIVVDSLKP YCDRVEGPPH DVLHRVQKML IDHLSGFVPM NISSETSMLS
1360 1370 1380 1390 1400
AFHKLNHDTS CGPYLGGRKK DHMVNGEPDK QLLDLLSSKW KLATQGIALP
1410 1420 1430 1440 1450
HEYTIGLKDE LRPIEKVQEG KRRMIWGCDV GVATVCAAAF KGVSDAITAN
1460 1470 1480 1490 1500
HQYGPIQVGI NMDSPSVEVL YQRIKSAAKV FAVDYSKWDS TQSPRVSAAS
1510 1520 1530 1540 1550
IDILRYFSDR SPIVDSAANT LKSPPIAIFN GVAVKVASGL PSGMPLTSVI
1560 1570 1580 1590 1600
NSLNHCMYVG CAILQSLEAR QIPVTWNLFS SFDMMTYGDD GVYMFPTMFA
1610 1620 1630 1640 1650
SVSDQIFGNL SAYGLKPTRV DKSVGAIESI DPESVVFLKR TITRTPNGIR
1660 1670 1680 1690 1700
GLLDRSSIIR QFFYIKGENS DDWKTPPKTI DPTSRGQQLW NACLYASQHG
1710 1720 1730 1740 1750
VEFYNKVLKL AMRAVEYEGL HLKPPSYSSA LEHYNSQFNG VEARSDQINM
1760
SDVTALHCDV FEV
Length:1,763
Mass (Da):194,988
Last modified:July 1, 2008 - v2
Checksum:i173626D6C862E46C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1417V → M in BAA14370 (PubMed:1853578).Curated1
Sequence conflicti1485 – 1487YSK → FSN in BAA14370 (PubMed:1853578).Curated3

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31836 Genomic RNA. Translation: BAA06622.2.
D90357 Genomic RNA. Translation: BAA14370.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31836 Genomic RNA. Translation: BAA06622.2.
D90357 Genomic RNA. Translation: BAA14370.1.

3D structure databases

ProteinModelPortaliP27408.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC24.002.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di3.40.50.300. 4 hits.
InterProiIPR003593. AAA+_ATPase.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR009003. Peptidase_S1_PA.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[Graphical view]
PfamiPF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 4 hits.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_FCVF4
AccessioniPrimary (citable) accession number: P27408
Secondary accession number(s): Q66913
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: July 1, 2008
Last modified: September 7, 2016
This is version 89 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

Complete proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.