P27409 (POLG_FCVF9) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Feline calicivirus (strain F9) (FCV) [Complete proteome]

Taxonomic identifier

11981 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Vesivirus › Feline calicivirus

Virus host

Felidae (cat family) [TaxID: 9681]

Protein attributes

Sequence length	1763 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

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 and eIF4G2 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 a 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 encodes 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 By similarity. 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.

Ontologies

Keywords
Biological process	Viral RNA replication
Ligand	ATP-binding Nucleotide-binding
Molecular function	Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
PTM	Covalent protein-RNA linkage Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1763	1763	Genome polyprotein		PRO_0000341997
	Chain	1 – 46	46	Protein p5.6 By similarity		PRO_0000036900
	Chain	47 – 331	285	Protein p32 By similarity		PRO_0000036901
	Chain	332 – 685	354	NTPase By similarity		PRO_0000036902
	Chain	686 – 960	275	Protein p30 By similarity		PRO_0000036903
	Chain	961 – 1071	111	Viral genome-linked protein By similarity		PRO_0000036904
	Chain	1072 – 1763	692	Protease-polymerase p76 By similarity		PRO_0000036905
Regions
	Domain	458 – 614	157	SF3 helicase
	Domain	1095 – 1199	105	Peptidase C24
	Domain	1478 – 1603	126	RdRp catalytic
	Nucleotide binding	484 – 491	8	ATP Potential
Sites
	Active site	1110	1	For protease activity By similarity
	Active site	1131	1	For protease activity By similarity
	Active site	1193	1	For protease activity By similarity
	Site	46 – 47	2	Cleavage; by Pro-Pol By similarity
	Site	331 – 332	2	Cleavage; by Pro-Pol By similarity
	Site	685 – 686	2	Cleavage; by Pro-Pol By similarity
	Site	960 – 961	2	Cleavage; by Pro-Pol By similarity
	Site	1071 – 1072	2	Cleavage; by Pro-Pol By similarity
Amino acid modifications
	Modified residue	984	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	P27409 [UniParc]. Last modified August 1, 1992. Version 1. Checksum: BE3C34FD49F35D9B	FASTA	1,763	195,029
	10 20 30 40 50 60 MSQTLSFVLK THSVRKDFVH SVKLTLARRR DLQYIYNKLS RTIRAEACPS CASYDVCPNC 70 80 90 100 110 120 TSGDVPDDGS STMSIPSWED VTKSSTYSLL LSEDTSDELC PEDLVNVAAH IRKALSTQSH 130 140 150 160 170 180 PANAEMCKEQ LTFLLVMAEA MLPQRSRASI PLHQQHTAAR LEWREKFFSK PLDFLLERVG 190 200 210 220 230 240 VSKDILQTTA IWKIILEKAC YCKSYGEQWF TAAKQKLREM KNFESDTLKP LIGGFIDGLR 250 260 270 280 290 300 FLTVDNPNPM GFLPKLIGLV KPLNLAMIID NHENTISGWI ITLTAIMELY NITECTIDII 310 320 330 340 350 360 TSVITAFYDK IGKATKFYSC VKALFTGFRS EDVANSFWYM AAAILCYLIT GLIPNNGRFS 370 380 390 400 410 420 KIKACLAGAT TLVSGIVATQ KLAAMFATWN SESIVNELSA RTVALSELNN PTTTSDTDSV 430 440 450 460 470 480 ERLLELAKIL HEEIKIHTLN 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 NPFVESHKRA RPGTSVPRSC YKKNFSHLSL AKRGAECWCK EYVLDPKGLQ HQSMKAPPPT 670 680 690 700 710 720 FLNIDSLAQT MKQDFLLKNM AFEAEDGCAE HRYGFVCQQE EVETVRRLLN AVRARMNATF 730 740 750 760 770 780 TVCVGPETSH SIGCTAHVLT PNETFNGKKF VVSRCNEASL SALEGNCVKS ALGVCMSDKD 790 800 810 820 830 840 LTHLCHFIKG KIVNDSVRLD ELPANQHVVT VNSVFDLAWA VRRHLTLAGQ FQAIRAAYDV 850 860 870 880 890 900 LTVPDKIPAM LRHWMDETSF SDDHVVTQFV TPGGIVILES CGGARIWALG RNVIRAGGVT 910 920 930 940 950 960 ATPTGGCVRL MGLSAPTMPW SEIFRELFSL LGRIWSSVKV SALVLTALGM YASRFRPKSE 970 980 990 1000 1010 1020 AKGKTKLKIG TYRGRGVALT DDEYDEWREH NASRKLDLSV EDFLMLRHRA ALGADDNDAV 1030 1040 1050 1060 1070 1080 KFRSWWNSRT KMANDYEDVT VIGKGGVKHE KIRTNTLKAV DRGYDVSFAE ESGPGTKFHK 1090 1100 1110 1120 1130 1140 NAIGSVTDVC GEHKGYCIHM GHGVYASVAH VVKGDSFFLG ERIFDLKTNG EFCCFRSTKI 1150 1160 1170 1180 1190 1200 LPSAAPFFSG KPTRDPWGSP VATEWKPKMY TTTSGKILGC FATTSTETHP GDCGLPYIDD 1210 1220 1230 1240 1250 1260 NGRVTGLHTG SGGPKTPSAK LVVPYVHIDM KTKSVTAQKY DVTKPDISYK GLICKQLDEI 1270 1280 1290 1300 1310 1320 RIIPKGTRLH VSPAHTEDYQ ECSHQPASLG SGDPRCPKSL TAIVVDSLKP YCENVEGPPH 1330 1340 1350 1360 1370 1380 DVLHRVQKML IDHLSGFVPM NISSETSMLS AFHKLNHDTS CGPYLGGRKK DHMANGEPDK 1390 1400 1410 1420 1430 1440 QLLDLLSAKW KLATQGIALP HEYTIGLKDE LRPVEKVSEG KRRMIWGCDV GVATVCAAAF 1450 1460 1470 1480 1490 1500 KGVSDAITAN HQYGPIQVGI NMDSPSVEAL FQRIKSAAKV FAVDYSKWDS TQSPRVSAAS 1510 1520 1530 1540 1550 1560 IDILRYFSDR SPIVDSASNT LKSPPVAIFN GVAVKVSSGL PSGMPLTSVI NSLNHCLYVG 1570 1580 1590 1600 1610 1620 CAILQSLEAK AIPVTWNLFS TFDIMTYGDD GVYMFPIMYA SISDQIFGNL SSYGLKPTRV 1630 1640 1650 1660 1670 1680 DKSVGAIEPI DPDSVVFLKR TITRTPQGIR GLLDRSSIIR QFYYIKGENS DDWKSPPKHI 1690 1700 1710 1720 1730 1740 DPTSRGQQLW NACLYASQHG LEFFNKVYRL AERAVEYEEL HFEPPTYASA LDHYNSQFNG 1750 1760 VEARSDQIDS SGMTALHCDV FEV

References

[1]	"The complete nucleotide sequence of a feline calicivirus." Carter M.J., Milton I.D., Meanger J., Bennett M., Gaskell R.M., Turner P.C. Virology 190:443-448(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Cloning and sequence determination of the feline calicivirus strain F9." Meanger J., Carter M.J., Gaskell R.M., Turner P.C. Biochem. Soc. Trans. 20:26S-26S(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	"Identification and sequence determination of the capsid protein gene of feline calicivirus." Carter M.J., Milton I.D., Turner P.C., Meanger J., Bennett M., Gaskell R.M. Arch. Virol. 122:223-235(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1098-1763.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M86379 Genomic RNA. Translation: AAA79326.1. Z11536 Genomic RNA. Translation: CAA77635.1.
PIR	RRWWF9. A43382.
3D structure databases
ProteinModelPortal	P27409.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR003593. AAA+_ATPase. IPR004004. Helic/Pol/Pept_Calicivir-typ. IPR000605. Helicase_SF3_ssDNA/RNA_vir. IPR014759. Helicase_SF3_ssRNA_vir. IPR000317. Peptidase_C24. IPR001205. RNA-dir_pol_C. IPR007094. RNA-dir_pol_PSvirus. IPR009003. Trypsin-like_Pept_dom. [Graphical view]
Pfam	PF03510. Peptidase_C24. 1 hit. PF00680. RdRP_1. 1 hit. PF00910. RNA_helicase. 1 hit. [Graphical view]
PRINTS	PR00916. 2CENDOPTASE. PR00918. CALICVIRUSNS.
SMART	SM00382. AAA. 1 hit. [Graphical view]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	PS50507. RDRP_SSRNA_POS. 1 hit. PS51218. SF3_HELICASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_FCVF9

Accession

Primary (citable) accession number: P27409

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1992
Last sequence update:	August 1, 1992
Last modified:	May 1, 2013
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program