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P27408

- POLG_FCVF4

UniProt

P27408 - POLG_FCVF4

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Protein
Genome polyprotein
Gene
ORF1
Organism
Feline calicivirus (strain Japanese F4) (FCV)
Status
Reviewed - 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.
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.
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.

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
Sitei46 – 472Cleavage; by Pro-Pol By similarity
Sitei331 – 3322Cleavage; by Pro-Pol By similarity
Sitei685 – 6862Cleavage; by Pro-Pol By similarity
Sitei960 – 9612Cleavage; by Pro-Pol By similarity
Sitei1071 – 10722Cleavage; by Pro-Pol By similarity
Active sitei1110 – 11101For protease activity1 Publication
Active sitei1131 – 11311For protease activity1 Publication
Active sitei1193 – 11931For protease activity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi484 – 4918ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. RNA binding Source: InterPro
  3. RNA helicase activity Source: InterPro
  4. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  5. cysteine-type endopeptidase activity Source: InterPro

GO - Biological processi

  1. RNA-protein covalent cross-linking Source: UniProtKB-KW
  2. suppression by virus of host translation Source: UniProtKB-KW
  3. transcription, DNA-templated Source: InterPro
  4. 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

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 positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostiFelidae (cat family) [TaxID: 9681]
ProteomesiUP000008668: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1079 – 10791H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1093 – 10931H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1099 – 10991H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1102 – 11021H → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1110 – 11101H → A: Complete loss of protease activity in vitro. 1 Publication
Mutagenesisi1121 – 11211E → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1125 – 11251D → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1131 – 11311E → A: Complete loss of protease activity in vitro. 1 Publication
Mutagenesisi1155 – 11551D → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1164 – 11641E → A: No effect on protease activity in vitro. 1 Publication
Mutagenesisi1193 – 11931C → A: Complete loss of protease activity in vitro. 1 Publication
Mutagenesisi1208 – 12081H → A: Complete loss of protease activity in vitro. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 17631763Genome polyprotein
PRO_0000341991Add
BLAST
Chaini1 – 4646Protein p5.6
PRO_0000341992Add
BLAST
Chaini47 – 331285Protein p32
PRO_0000341993Add
BLAST
Chaini332 – 685354NTPase
PRO_0000341994Add
BLAST
Chaini686 – 960275Protein p30
PRO_0000341995Add
BLAST
Chaini961 – 1071111Viral genome-linked protein
PRO_0000341996Add
BLAST
Chaini1072 – 1763692Protease-polymerase p76
PRO_0000036899Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei984 – 9841O-(5'-phospho-RNA)-tyrosine By similarity

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.

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.

Structurei

3D structure databases

ProteinModelPortaliP27408.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini458 – 614157SF3 helicase
Add
BLAST
Domaini1095 – 1199105Peptidase C24
Add
BLAST
Domaini1478 – 1603126RdRp catalytic
Add
BLAST

Domaini

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

Sequence similaritiesi

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.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[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

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MSQTLSFVLK THSVRKDFVH SVKVTLARRR DLQYLYNKLA RTMRAEACPS     50
CSSYDVCPNC TSSDIPDNGS STTSIPSWED VTKTSTYSLL LSEDTSDELC 100
PDDLVNVAAH IRKALSTQAH PANTEMCKEQ LTSLLVMAEA MLPQRSRASI 150
PLHQQHQAAR LEWREKFFSK PLDFLLERIG VSKDILQITA IWKIILEKAC 200
YCKSYGEQWF CAAKQKLREM RTFESDTLKP LVGAFIDGLR FMTVDNPNPM 250
GFLPKLIGLV KPLNLAMIID NHENTLSGWV VTLTAIMELY NITECTIDVI 300
TSLVTGFYDK ISKATKFFSQ VKALFTGFRS EDVANSFWYM AAAILCYLIT 350
GLIPNNGRFS KIKACLSGAT TLVSGIIATQ KLAAMFATWN SESIVNELSA 400
RTVAISELNN PTTTSDTDSV ERLLELAKIL HEEIKVHTLN PIMQSYNPIL 450
RNLMSTLDGV ITSCNKRKAI ARKRQVPVCY ILTGPPGCGK TTAAQALAKK 500
LSDQEPSVIN LDVDHHDTYT GNEVCIIDEF DSSDKVDYAN FVIGMVNSAP 550
MVLNCDMLEN KGKLFTSKYI IMTSNSETPV KPSSKRAGAF YRRVTIIDVT 600
NPLVESHKRA RPGTSVPRSC YKKNFSHLSL AKRGAECWCK EYVLDPKGLQ 650
HQTIKAPPPT FLNIDSLAQT MKQDFVLKNM AFEAEDGCSE HRYGFICQQS 700
EVETVRRLLN AIRARLNATF TVCVGPEASH SIGCTAHVLT PDEPFNGRRF 750
IVSRCNEASL AALEGNCVQS ALGVCMSNKD LTHLCHFIRG KIVNDSVRLD 800
ELPANQHVVT VNSVFDLAWA LRRHLTLTGQ FQAIRAAYDV LTVPDKVPAM 850
LRHWMDETSF SDEHVVTQFV TPGGVVILES CGGARIWALG HNVIRAGGVT 900
ATPTGGCVRL VGLSAQTLPW SEIFRELFTL LGRIWSSIKV STLVLTALGM 950
YASRFRPKSE AKGKTKSKIG PYRGRGVALT DDEYDEWREH NANRKLDLSV 1000
EDFLMLRHRA ALGADDADAV KFRSWWNSRT RPGDGFEDVT VIGKGGVKHE 1050
KIRTSTLRAV DRGYDVSFAE ESGPGTKFHK NAIGSVTDVC GEHKGYCVHM 1100
GHGVYASVAH VVKGDSYFLG ERIFDVKTNG EFCCFRSTKI LPSAAPFFSG 1150
KPTRDPWGSP VATEWKPKAY TTTSGKIVGC FATTSTETHP GDCGLPYIDD 1200
NGRVTGLHTG SGGPKTPSAK LVVPYIHIDM KNKSVTPQKY DETKPNISYK 1250
GLVCKQLDEI RIIPKGTRLH VSPAHVDDFE ECSHQPASLG SGDPRCPKSL 1300
TAIVVDSLKP YCDRVEGPPH DVLHRVQKML IDHLSGFVPM NISSETSMLS 1350
AFHKLNHDTS CGPYLGGRKK DHMVNGEPDK QLLDLLSSKW KLATQGIALP 1400
HEYTIGLKDE LRPIEKVQEG KRRMIWGCDV GVATVCAAAF KGVSDAITAN 1450
HQYGPIQVGI NMDSPSVEVL YQRIKSAAKV FAVDYSKWDS TQSPRVSAAS 1500
IDILRYFSDR SPIVDSAANT LKSPPIAIFN GVAVKVASGL PSGMPLTSVI 1550
NSLNHCMYVG CAILQSLEAR QIPVTWNLFS SFDMMTYGDD GVYMFPTMFA 1600
SVSDQIFGNL SAYGLKPTRV DKSVGAIESI DPESVVFLKR TITRTPNGIR 1650
GLLDRSSIIR QFFYIKGENS DDWKTPPKTI DPTSRGQQLW NACLYASQHG 1700
VEFYNKVLKL AMRAVEYEGL HLKPPSYSSA LEHYNSQFNG VEARSDQINM 1750
SDVTALHCDV FEV 1763
Length:1,763
Mass (Da):194,988
Last modified:July 1, 2008 - v2
Checksum:i173626D6C862E46C
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1417 – 14171V → M in BAA14370. 1 Publication
Sequence conflicti1485 – 14873YSK → FSN in BAA14370. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D31836 Genomic RNA. Translation: BAA06622.2.
D90357 Genomic RNA. Translation: BAA14370.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D31836 Genomic RNA. Translation: BAA06622.2 .
D90357 Genomic RNA. Translation: BAA14370.1 .

3D structure databases

ProteinModelPortali P27408.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi C24.002.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

Gene3Di 3.40.50.300. 4 hits.
InterProi IPR003593. 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.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view ]
Pfami PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view ]
PRINTSi PR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTi SM00382. AAA. 1 hit.
[Graphical view ]
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 4 hits.
PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "The molecular cloning and sequence of an open reading frame encoding for non-structural proteins of feline calicivirus F4 strain isolated in Japan."
    Oshikamo R., Tohya Y., Kawaguchi Y., Tomonaga K., Maeda K., Takeda N., Utagawa E., Kai C., Mikami T.
    J. Vet. Med. Sci. 56:1093-1099(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1383-1763.
  3. "Highly conserved configuration of catalytic amino acid residues among calicivirus-encoded proteases."
    Oka T., Yamamoto M., Yokoyama M., Ogawa S., Hansman G.S., Katayama K., Miyashita K., Takagi H., Tohya Y., Sato H., Takeda N.
    J. Virol. 81:6798-6806(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACTIVE SITES, MUTAGENESIS OF HIS-1079; HIS-1093; HIS-1099; HIS-1102; HIS-1110; GLU-1121; ASP-1125; GLU-1131; ASP-1155; GLU-1164; CYS-1193 AND HIS-1208.

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: July 9, 2014
This is version 81 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

External Data

Dasty 3

Similar proteinsi