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P18247

- POLG_PVYN

UniProt

P18247 - POLG_PVYN

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Protein
Genome polyprotein
Gene
N/A
Organism
Potato virus Y (strain N) (PVY)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

Capsid protein: involved in aphid transmission, cell-to-cell and systemis movement, encapsidation of the viral RNA and in the regulation of viral RNA amplification.1 Publication
Nuclear inclusion protein B: an RNA-dependent RNA polymerase that plays an essential role in the virus replication.1 Publication
Helper component proteinase: required for aphid transmission and also has proteolytic activity. Only cleaves a Gly-Gly dipeptide at its own C-terminus. Interacts with virions and aphid stylets. Acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. May have RNA-binding activity.1 Publication
Cytoplasmic inclusion protein: has helicase activity. It may be involved in replication.1 Publication
Both 6K peptides are indispensable for virus replication By similarity.1 Publication
Nuclear inclusion protein A: has RNA-binding and proteolytic activities.1 Publication

Catalytic activityi

Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei192 – 1921For P1 proteinase activity By similarity
Active sitei201 – 2011For P1 proteinase activity Reviewed prediction
Active sitei235 – 2351For P1 proteinase activity By similarity
Sitei284 – 2852Cleavage; by P1 proteinase Reviewed prediction
Active sitei626 – 6261For helper component proteinase activity By similarity
Active sitei699 – 6991For helper component proteinase activity By similarity
Sitei740 – 7412Cleavage; by HC-pro Reviewed prediction
Sitei1105 – 11062Cleavage; by NIa-pro By similarity
Sitei1157 – 11582Cleavage; by NIa-pro By similarity
Sitei1791 – 17922Cleavage; by NIa-pro By similarity
Sitei1843 – 18442Cleavage; by NIa-pro By similarity
Sitei2031 – 20322Cleavage; by NIa-pro By similarity
Active sitei2077 – 20771For nuclear inclusion protein A activity By similarity
Active sitei2112 – 21121For nuclear inclusion protein A activity By similarity
Active sitei2182 – 21821For nuclear inclusion protein A activity By similarity
Sitei2275 – 22762Cleavage; by NIa-pro By similarity
Sitei2796 – 27972Cleavage; by NIa-pro By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1242 – 12498ATP Reviewed prediction

GO - Molecular functioni

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

Helicase, Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Suppressor of RNA silencing, Thiol protease, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi3.4.22.45. 5005.

Protein family/group databases

MEROPSiC04.002.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 10 chains:
Alternative name(s):
N-terminal protein
Helper component proteinase (EC:3.4.22.45)
Short name:
HC-pro
6 kDa protein 1
Short name:
6K1
6 kDa protein 2
Short name:
6K2
Alternative name(s):
VPg
Nuclear inclusion protein A (EC:3.4.22.44)
Short name:
NI-a
Short name:
NIa
Alternative name(s):
49 kDa proteinase
Short name:
49 kDa-Pro
NIa-pro
Nuclear inclusion protein B (EC:2.7.7.48)
Short name:
NI-b
Short name:
NIb
Alternative name(s):
RNA-directed RNA polymerase
Capsid protein
Short name:
CP
Alternative name(s):
Coat protein
OrganismiPotato virus Y (strain N) (PVY)
Taxonomic identifieri12219 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stagePotyviridaePotyvirus
Virus hostiCapsicum (peppers) [TaxID: 4071]
Nicotiana [TaxID: 4085]
Solanum lycopersicum (Tomato) (Lycopersicon esculentum) [TaxID: 4081]
Solanum tuberosum (Potato) [TaxID: 4113]
ProteomesiUP000000520: Genome

Subcellular locationi

Chain Capsid protein : Virion Reviewed prediction

GO - Cellular componenti

  1. helical viral capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Helical capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 30633063Genome polyprotein
PRO_0000420017Add
BLAST
Chaini1 – 284284P1 proteinase Reviewed prediction
PRO_0000040407Add
BLAST
Chaini285 – 740456Helper component proteinase Reviewed prediction
PRO_0000040408Add
BLAST
Chaini741 – 1105365Protein P3 By similarity
PRO_0000040409Add
BLAST
Chaini1106 – 1157526 kDa protein 1 By similarity
PRO_0000040410Add
BLAST
Chaini1158 – 1791634Cytoplasmic inclusion protein By similarity
PRO_0000040411Add
BLAST
Chaini1792 – 1843526 kDa protein 2 By similarity
PRO_0000040412Add
BLAST
Chaini1844 – 2031188Viral genome-linked protein By similarity
PRO_0000040413Add
BLAST
Chaini2032 – 2275244Nuclear inclusion protein A By similarity
PRO_0000040414Add
BLAST
Chaini2276 – 2796521Nuclear inclusion protein B By similarity
PRO_0000040415Add
BLAST
Chaini2797 – 3063267Capsid protein By similarity
PRO_0000040416Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1907 – 19071O-(5'-phospho-RNA)-tyrosine By similarity

Post-translational modificationi

VPg is uridylylated by the polymerase and is covalently attached to the 5'-end of the genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity.
Potyviral RNA is expressed as two polyproteins which undergo post-translational proteolytic processing. Genome polyprotein is processed by NIa-pro, P1 and HC-pro proteinases resulting in the production of at least ten individual proteins. P3N-PIPO polyprotein is cleaved by P1 and HC-pro proteinases resulting in the production of three individual proteins. The P1 proteinase and the HC-pro cleave only their respective C-termini autocatalytically. 6K1 is essential for proper proteolytic separation of P3 from CI By similarity.

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Structurei

3D structure databases

ProteinModelPortaliP18247.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1229 – 1381153Helicase ATP-binding
Add
BLAST
Domaini1400 – 1559160Helicase C-terminal
Add
BLAST
Domaini2032 – 2250219Peptidase C4
Add
BLAST
Domaini2519 – 2643125RdRp catalytic
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi334 – 3374Involved in interaction with stylet and aphid transmission By similarity
Motifi592 – 5943Involved in virions binding and aphid transmission By similarity
Motifi1331 – 13344DECH box
Motifi1884 – 18929Nuclear localization signal Reviewed prediction

Domaini

The N-terminus of helper component proteinase is involved in interaction with stylets. The central part is involved in interaction with virions and the C-terminus is involved in cell-to cell movement of the virus.

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR001456. Peptidase_C6.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00863. Peptidase_C4. 1 hit.
PF00851. Peptidase_C6. 1 hit.
PF01577. Peptidase_S30. 1 hit.
PF00767. Poty_coat. 1 hit.
PF08440. Poty_PP. 1 hit.
PF00680. RdRP_1. 1 hit.
[Graphical view]
PRINTSiPR00966. NIAPOTYPTASE.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51436. POTYVIRUS_NIA_PRO. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

Isoform Genome polyprotein (identifier: P18247-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

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MATYMSTICF GSFECKLPYS PASCEHIVKE REVPASVDPF ADLETQLSAR     50
LLKQKYATVR VLKNGTFTYR YKTDAQIMRI QKKLERKDRE EYHFQMAAPS 100
IVSKITIAGG DPPSKSEPQA PRGIIHTTPR MRKVKTRPII KLTEGQMNHL 150
IKQIKQIMSE KRGSVHLISK KTTHVQYKKI LGAYSAAVRT AHMMGLRRRV 200
DFRCDMWTVG LLQRLARTDK WSNQVRTINI RRGDSGVILN TKSLKGHFGR 250
SSGGLFIVRG SHEGKLYDAR SRVTQSILNS MIQFSNADNF WKGLDGNWAR 300
MRYPSDHTCV AGLPVEDCGR VAALMAHSIL PCYKITCPTC AQQYASLPVS 350
DLFKLLHKHA RDGLNRLGAD KDRFIHVNKF LIALEHLTEP VDLNLELFNE 400
IFKSIGEKQQ APFKNLNVLN NFFLKGKENT AHEWQVAQLS LLELARFQKN 450
RTDNIKKGDI SFFRNKLSAK ANWNLYLSCD NQLDKNANFL WGQREYHAKR 500
FFSNFFEEID PAKGYSAYEI RKHPSGTRKL SIGNLVVPLD LAEFRQKMKG 550
DYRKQPGVSK KCTSSKDGNY VYPCCCTTLD DGSAIESTFY PPTKKHLVIG 600
NSGDQKFVDL PKGDSEMLYI AKQGYCYINV FLAMLINISE EDAKDFTKKV 650
RDMCVPKLGT WPTMMDLATT CAQMRIFYPD VHDAELPRIL VDHDTQTCHV 700
VDSFGSQTTG YHILKASSVS QLILFANDEL ESDIKHYRVG GVPNASPELG 750
STISPFREGG VIMSESAALK LLLKGIFRPK VMRQLLLDEP YLLILSILSP 800
GILMAMYNNG IFELAVRLWI NEKQSIAMIA SLLSALALRV SAAETLVAQR 850
IIIDAAATDL LDATCDGFNL HLTYPTALMV LQVVKNRNEC DDTLFKAGFP 900
SYNTSVVQIM EKNYLNLLND AWKDLTWREN YPQHGTHTEQ NALSTRYIKP 950
TEKADLKGLY NISPQAFLGR SAQVVKGTAS GLSERFNNYF NTKCVNISSF 1000
FIRRIFRRLP TFVTFVNSLL VISMLTSVVA VCQAIILDQR KYRREIELMQ 1050
IEKNEIVCME LYASLQRKLE RDFTWDEYIE YLKSVNPQIV QFAQAQMEEY 1100
DVRHQRSTPV VKNLEQVVAF MALVIMVFDA ERSDCVFKTL NKFKGVLSSL 1150
DYEVRHQSLD DVIKNFDERN EIIDFELSED TIRTSSVLDT KFSDWWDRQI 1200
QMGHTLPHYR TEGHFMEFTR ATAVQVANDI AHSEHLDFLV RGAVGSGKST 1250
GLPVHLSVAG SVLLIEPTRP LAENVFKQLS SEPFFKKPTL RMRGNSIFGS 1300
SPISVMTSGF ALHYFANNRS QLAQFNFVIF DECHVLDPSA MAFRSLLSVY 1350
HQACKVLKVS ATPVGREVEF TTQQPVKLIV EDTVSFQSFV DAQGSKTNAD 1400
VVQFGSNVLV YVSSYNEVDT LAKLLTDKNM MVTKVDGRTM KHGCLEIVTK 1450
GTSARPHFVV ATNIIENGVT LDIDVVVDFG LKVSPFLDID NRSIAYNKVS 1500
VSYGERIQRL GRVGRFKKGV ALRIGHTEKG IIEIPSMVAT EAALACFAYN 1550
LPVMTGGVST SLIGNCTVRQ VKTMQQFELS PFFIQNFVAH DGSMHPVIHD 1600
ILKKYKLRDC MTPLCDQSIP YRASSTWLSV SEYERLGVAL EIPKQVKIAF 1650
HIKEIPPKLH EMLWETVVKY KDVCLFPSIR ASSISKIAYT LRTDLFAIPR 1700
TLILVERLLE EERVKQSQFR SLIDEGCSSM FSIVNLTNTL RARYAKDYTA 1750
ENIQKLEKVR SQLKEFSNLD GSACEENLIK RYESLQFVHH QAATSLAKDL 1800
KLKGIWNKSL VAKDLIIAGA VAIGGIGLIY SWFTQSVETV SHQGKNKSKR 1850
IQALKFRHAR DKRAGFEIDN NDDTIEEFFG SAYRKKGKGK GTTVGMGKSS 1900
RRFINMYGFD PTEYSFIQFV DPLTGRQIEE NVYADIRDIQ ERFSEVRKKM 1950
VENDDIEMQA LGSNTTIHAY FRKDWCDKAL KIDLMPHNPL KVCDKTNGIA 2000
KFPERELELR QTGPAVEVDV KDIPAQEVEH EAKSLMRGLR DFNPIAQTVC 2050
RLKVSVEYGA SEMYGFGFGA YIVANHHLFR SYNGSMEVQS MHGTFRVKNL 2100
HSLSVLPIKG RDIILIKMPK DFPVFPQKLH FRAPTQNERI CLVGTNFQEK 2150
YASSIITETS TTYNIPGSTF WKHWIETDNG HCGLPVVSTA DGCIVGIHSL 2200
ANNAHTTNYY SAFDEDFESK YLRTNEHNEW VKSWVYNPDT VLWGPLKLKD 2250
STPKGLFKTT KLVQDLIDHD VVVEQAKHSA WMFEALTGNL QAVATMKSQL 2300
VTKHVVKGEC RHFTEFLTVD AEAEAEAFFR PLMDAYGKSL LNRDAYIKDI 2350
MKYSKPIDVG VVDRMHLRKP SIGLSSTCNV HGFKKCAYVT DEQEIFKALN 2400
MKAAVGASYG CKKKDYFEHF TDADKEEIVM QSCLRLYKGL LGIWNGSLKA 2450
ELRCKEKILA NKTRTFTAAP LDTLLGGKVC VDDFNNQFYS KNIECCWTVG 2500
MTKFYGGWDK LLRRLPENWV YCDADGSQFD SSLTPYLINA VLTIRSTYME 2550
DWDVGLQMLR NLYTEIVYTP ISTPDGTIVK KFRGNNSGQP STVVDNSLMV 2600
VLAMHYALIK ECVEFEEIDS TCVFFVNGDD LLIAVNPEKE SILDRMSQHF 2650
SDLGLNYDFS SRTRRKEELW FMSHRGLLIE GMYVPKLEEE RIVSILQWDR 2700
ADLPEHRLEA ICAAMIESWG YSELTHQIRR FYSWLLQQQP FATIAQEGKA 2750
PYIASMALRK LYMDRAVDEE ELRAFTEMMV ALDDEFELDS YEVHHQANDT 2800
IDAGGSNKKD AKPEQGSIQP NPNKGKDKDV NAGTSGTHTV PRIKAITSKM 2850
RMPTSKGATV PNLEHLLEYA PQQIDISNTR ATQSQFDTWY EAVRMAYDIG 2900
ETEMPTVMNG LMVWCIENGT SPNVNGVWVM MDGNEQVEYP LKPIVENAKP 2950
TLRQIMAHFS DVAEAYIEMR NKKEPYMPRY GLIRNLRDMG LARYAFDFYE 3000
VTSRTPVRAR EAHIQMKAAA LKSAQPRLFG LDGGISTQEE NTERHTTEDV 3050
SPSMHTLLGV KNM 3063

Note: Produced by conventional translation.

Length:3,063
Mass (Da):347,539
Last modified:February 1, 1996 - v2
Checksum:i3EC79125DE33F1BB
GO
Isoform P3N-PIPO polyprotein (identifier: P0CJ93-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry P0CJ93.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by -1 ribosomal frameshifting in P3 ORF.

Length:986
Mass (Da):111,724
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X12456 Genomic RNA. Translation: CAA30988.1.
D00441 Genomic RNA. Translation: BAA00342.1.
PIRiJS0166.
RefSeqiNP_056759.1. NC_001616.1.

Genome annotation databases

GeneIDi1494052.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X12456 Genomic RNA. Translation: CAA30988.1 .
D00441 Genomic RNA. Translation: BAA00342.1 .
PIRi JS0166.
RefSeqi NP_056759.1. NC_001616.1.

3D structure databases

ProteinModelPortali P18247.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi C04.002.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 1494052.

Enzyme and pathway databases

BRENDAi 3.4.22.45. 5005.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR001456. Peptidase_C6.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view ]
Pfami PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00863. Peptidase_C4. 1 hit.
PF00851. Peptidase_C6. 1 hit.
PF01577. Peptidase_S30. 1 hit.
PF00767. Poty_coat. 1 hit.
PF08440. Poty_PP. 1 hit.
PF00680. RdRP_1. 1 hit.
[Graphical view ]
PRINTSi PR00966. NIAPOTYPTASE.
SMARTi SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view ]
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51436. POTYVIRUS_NIA_PRO. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Nucleotide sequence of potato virus Y (N Strain) genomic RNA."
    Robaglia C., Durand-Tardif M., Tronchet M., Boudazin G., Astier-Manifacier S., Casse-Delbart F.
    J. Gen. Virol. 70:935-947(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. Durand-Tardif M.
    Submitted (JAN-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants."
    Voinnet O., Pinto Y.M., Baulcombe D.C.
    Proc. Natl. Acad. Sci. U.S.A. 96:14147-14152(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. Cited for: REVIEW.

Entry informationi

Entry nameiPOLG_PVYN
AccessioniPrimary (citable) accession number: P18247
Secondary accession number(s): Q85266
, Q85267, Q85268, Q85269, Q85270, Q85271, Q85272, Q85273
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: February 1, 1996
Last modified: September 3, 2014
This is version 132 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, Reference 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