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P27408 (POLG_FCVF4) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 79. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 6 chains:

  1. Protein p5.6
  2. Protein p32
  3. NTPase
    EC=3.6.1.15
    Alternative name(s):
    p39
  4. Protein p30
  5. Viral genome-linked protein
    Alternative name(s):
    VPg
    p13
  6. Protease-polymerase p76
    Short name=Pro-Pol
    EC=2.7.7.48
    EC=3.4.22.66
Gene names
ORF Names:ORF1
OrganismFeline calicivirus (strain Japanese F4) (FCV) [Complete proteome]
Taxonomic identifier11980 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostFelidae (cat family) [TaxID: 9681]

Protein attributes

Sequence length1763 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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).

Subunit structure

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.

Domain

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

Post-translational modification

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.

Sequence similarities

Contains 1 peptidase C24 domain.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 17631763Genome polyprotein
PRO_0000341991
Chain1 – 4646Protein p5.6
PRO_0000341992
Chain47 – 331285Protein p32
PRO_0000341993
Chain332 – 685354NTPase
PRO_0000341994
Chain686 – 960275Protein p30
PRO_0000341995
Chain961 – 1071111Viral genome-linked protein
PRO_0000341996
Chain1072 – 1763692Protease-polymerase p76
PRO_0000036899

Regions

Domain458 – 614157SF3 helicase
Domain1095 – 1199105Peptidase C24
Domain1478 – 1603126RdRp catalytic
Nucleotide binding484 – 4918ATP Potential

Sites

Active site11101For protease activity Ref.3
Active site11311For protease activity Ref.3
Active site11931For protease activity Ref.3
Site46 – 472Cleavage; by Pro-Pol By similarity
Site331 – 3322Cleavage; by Pro-Pol By similarity
Site685 – 6862Cleavage; by Pro-Pol By similarity
Site960 – 9612Cleavage; by Pro-Pol By similarity
Site1071 – 10722Cleavage; by Pro-Pol By similarity

Amino acid modifications

Modified residue9841O-(5'-phospho-RNA)-tyrosine By similarity

Experimental info

Mutagenesis10791H → A: No effect on protease activity in vitro. Ref.3
Mutagenesis10931H → A: No effect on protease activity in vitro. Ref.3
Mutagenesis10991H → A: No effect on protease activity in vitro. Ref.3
Mutagenesis11021H → A: No effect on protease activity in vitro. Ref.3
Mutagenesis11101H → A: Complete loss of protease activity in vitro. Ref.3
Mutagenesis11211E → A: No effect on protease activity in vitro. Ref.3
Mutagenesis11251D → A: No effect on protease activity in vitro. Ref.3
Mutagenesis11311E → A: Complete loss of protease activity in vitro. Ref.3
Mutagenesis11551D → A: No effect on protease activity in vitro. Ref.3
Mutagenesis11641E → A: No effect on protease activity in vitro. Ref.3
Mutagenesis11931C → A: Complete loss of protease activity in vitro. Ref.3
Mutagenesis12081H → A: Complete loss of protease activity in vitro. Ref.3
Sequence conflict14171V → M in BAA14370. Ref.2
Sequence conflict1485 – 14873YSK → FSN in BAA14370. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P27408 [UniParc].

Last modified July 1, 2008. Version 2.
Checksum: 173626D6C862E46C

FASTA1,763194,988
        10         20         30         40         50         60 
MSQTLSFVLK THSVRKDFVH SVKVTLARRR DLQYLYNKLA RTMRAEACPS CSSYDVCPNC 

        70         80         90        100        110        120 
TSSDIPDNGS STTSIPSWED VTKTSTYSLL LSEDTSDELC PDDLVNVAAH IRKALSTQAH 

       130        140        150        160        170        180 
PANTEMCKEQ LTSLLVMAEA MLPQRSRASI PLHQQHQAAR LEWREKFFSK PLDFLLERIG 

       190        200        210        220        230        240 
VSKDILQITA IWKIILEKAC YCKSYGEQWF CAAKQKLREM RTFESDTLKP LVGAFIDGLR 

       250        260        270        280        290        300 
FMTVDNPNPM GFLPKLIGLV KPLNLAMIID NHENTLSGWV VTLTAIMELY NITECTIDVI 

       310        320        330        340        350        360 
TSLVTGFYDK ISKATKFFSQ VKALFTGFRS EDVANSFWYM AAAILCYLIT GLIPNNGRFS 

       370        380        390        400        410        420 
KIKACLSGAT TLVSGIIATQ KLAAMFATWN SESIVNELSA RTVAISELNN PTTTSDTDSV 

       430        440        450        460        470        480 
ERLLELAKIL HEEIKVHTLN PIMQSYNPIL RNLMSTLDGV ITSCNKRKAI ARKRQVPVCY 

       490        500        510        520        530        540 
ILTGPPGCGK TTAAQALAKK LSDQEPSVIN LDVDHHDTYT GNEVCIIDEF DSSDKVDYAN 

       550        560        570        580        590        600 
FVIGMVNSAP MVLNCDMLEN KGKLFTSKYI IMTSNSETPV KPSSKRAGAF YRRVTIIDVT 

       610        620        630        640        650        660 
NPLVESHKRA RPGTSVPRSC YKKNFSHLSL AKRGAECWCK EYVLDPKGLQ HQTIKAPPPT 

       670        680        690        700        710        720 
FLNIDSLAQT MKQDFVLKNM AFEAEDGCSE HRYGFICQQS EVETVRRLLN AIRARLNATF 

       730        740        750        760        770        780 
TVCVGPEASH SIGCTAHVLT PDEPFNGRRF IVSRCNEASL AALEGNCVQS ALGVCMSNKD 

       790        800        810        820        830        840 
LTHLCHFIRG KIVNDSVRLD ELPANQHVVT VNSVFDLAWA LRRHLTLTGQ FQAIRAAYDV 

       850        860        870        880        890        900 
LTVPDKVPAM LRHWMDETSF SDEHVVTQFV TPGGVVILES CGGARIWALG HNVIRAGGVT 

       910        920        930        940        950        960 
ATPTGGCVRL VGLSAQTLPW SEIFRELFTL LGRIWSSIKV STLVLTALGM YASRFRPKSE 

       970        980        990       1000       1010       1020 
AKGKTKSKIG PYRGRGVALT DDEYDEWREH NANRKLDLSV EDFLMLRHRA ALGADDADAV 

      1030       1040       1050       1060       1070       1080 
KFRSWWNSRT RPGDGFEDVT VIGKGGVKHE KIRTSTLRAV DRGYDVSFAE ESGPGTKFHK 

      1090       1100       1110       1120       1130       1140 
NAIGSVTDVC GEHKGYCVHM GHGVYASVAH VVKGDSYFLG ERIFDVKTNG EFCCFRSTKI 

      1150       1160       1170       1180       1190       1200 
LPSAAPFFSG KPTRDPWGSP VATEWKPKAY TTTSGKIVGC FATTSTETHP GDCGLPYIDD 

      1210       1220       1230       1240       1250       1260 
NGRVTGLHTG SGGPKTPSAK LVVPYIHIDM KNKSVTPQKY DETKPNISYK GLVCKQLDEI 

      1270       1280       1290       1300       1310       1320 
RIIPKGTRLH VSPAHVDDFE ECSHQPASLG SGDPRCPKSL TAIVVDSLKP YCDRVEGPPH 

      1330       1340       1350       1360       1370       1380 
DVLHRVQKML IDHLSGFVPM NISSETSMLS AFHKLNHDTS CGPYLGGRKK DHMVNGEPDK 

      1390       1400       1410       1420       1430       1440 
QLLDLLSSKW KLATQGIALP HEYTIGLKDE LRPIEKVQEG KRRMIWGCDV GVATVCAAAF 

      1450       1460       1470       1480       1490       1500 
KGVSDAITAN HQYGPIQVGI NMDSPSVEVL YQRIKSAAKV FAVDYSKWDS TQSPRVSAAS 

      1510       1520       1530       1540       1550       1560 
IDILRYFSDR SPIVDSAANT LKSPPIAIFN GVAVKVASGL PSGMPLTSVI NSLNHCMYVG 

      1570       1580       1590       1600       1610       1620 
CAILQSLEAR QIPVTWNLFS SFDMMTYGDD GVYMFPTMFA SVSDQIFGNL SAYGLKPTRV 

      1630       1640       1650       1660       1670       1680 
DKSVGAIESI DPESVVFLKR TITRTPNGIR GLLDRSSIIR QFFYIKGENS DDWKTPPKTI 

      1690       1700       1710       1720       1730       1740 
DPTSRGQQLW NACLYASQHG VEFYNKVLKL AMRAVEYEGL HLKPPSYSSA LEHYNSQFNG 

      1750       1760 
VEARSDQINM SDVTALHCDV FEV 

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References

[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]"Sequence analysis of the 3'-end of feline calicivirus genome."
Tohya Y., Taniguchi Y., Takahashi E., Utagawa E., Takeda N., Miyamura K., Yamazaki S., Mikami T.
Virology 183:810-814(1991) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D31836 Genomic RNA. Translation: BAA06622.2.
D90357 Genomic RNA. Translation: BAA14370.1.

3D structure databases

ProteinModelPortalP27408.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSC24.002.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.40.50.300. 4 hits.
InterProIPR003593. 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]
PfamPF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 4 hits.
PROSITEPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLG_FCVF4
AccessionPrimary (citable) accession number: P27408
Secondary accession number(s): Q66913
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: July 1, 2008
Last modified: April 16, 2014
This is version 79 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries