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P18247 (POLG_PVYN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 130. 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 10 chains:

  1. P1 proteinase
    EC=3.4.-.-
    Alternative name(s):
    N-terminal protein
  2. Helper component proteinase
    Short name=HC-pro
    EC=3.4.22.45
  3. Protein P3
  4. 6 kDa protein 1
    Short name=6K1
  5. Cytoplasmic inclusion protein
    Short name=CI
    EC=3.6.4.-
  6. 6 kDa protein 2
    Short name=6K2
  7. Viral genome-linked protein
    Alternative name(s):
    VPg
  8. Nuclear inclusion protein A
    Short name=NI-a
    Short name=NIa
    EC=3.4.22.44
    Alternative name(s):
    49 kDa proteinase
    Short name=49 kDa-Pro
    NIa-pro
  9. Nuclear inclusion protein B
    Short name=NI-b
    Short name=NIb
    EC=2.7.7.48
    Alternative name(s):
    RNA-directed RNA polymerase
  10. Capsid protein
    Short name=CP
    Alternative name(s):
    Coat protein
OrganismPotato virus Y (strain N) (PVY) [Reference proteome]
Taxonomic identifier12219 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stagePotyviridaePotyvirus
Virus hostCapsicum (peppers) [TaxID: 4071]
Nicotiana [TaxID: 4085]
Solanum lycopersicum (Tomato) (Lycopersicon esculentum) [TaxID: 4081]
Solanum tuberosum (Potato) [TaxID: 4113]

Protein attributes

Sequence length3063 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

Function

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. Ref.3

Nuclear inclusion protein B: an RNA-dependent RNA polymerase that plays an essential role in the virus replication. Ref.3

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. Ref.3

Cytoplasmic inclusion protein: has helicase activity. It may be involved in replication. Ref.3

Both 6K peptides are indispensable for virus replication By similarity. Ref.3

Nuclear inclusion protein A: has RNA-binding and proteolytic activities. Ref.3

Catalytic activity

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.

Subcellular location

Capsid protein: Virion Potential.

Domain

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.

Post-translational modification

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.

Sequence similarities

Belongs to the potyviridae genome polyprotein family.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Contains 1 peptidase C4 domain.

Contains 1 peptidase C6 domain.

Contains 1 peptidase S30 domain.

Contains 1 RdRp catalytic domain.

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]
Isoform Genome polyprotein (identifier: P18247-1)

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.
Note: Produced by conventional translation.
Isoform P3N-PIPO polyprotein (identifier: P0CJ93-1)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 30633063Genome polyprotein
PRO_0000420017
Chain1 – 284284P1 proteinase Potential
PRO_0000040407
Chain285 – 740456Helper component proteinase Potential
PRO_0000040408
Chain741 – 1105365Protein P3 By similarity
PRO_0000040409
Chain1106 – 1157526 kDa protein 1 By similarity
PRO_0000040410
Chain1158 – 1791634Cytoplasmic inclusion protein By similarity
PRO_0000040411
Chain1792 – 1843526 kDa protein 2 By similarity
PRO_0000040412
Chain1844 – 2031188Viral genome-linked protein By similarity
PRO_0000040413
Chain2032 – 2275244Nuclear inclusion protein A By similarity
PRO_0000040414
Chain2276 – 2796521Nuclear inclusion protein B By similarity
PRO_0000040415
Chain2797 – 3063267Capsid protein By similarity
PRO_0000040416

Regions

Domain1229 – 1381153Helicase ATP-binding
Domain1400 – 1559160Helicase C-terminal
Domain2032 – 2250219Peptidase C4
Domain2519 – 2643125RdRp catalytic
Nucleotide binding1242 – 12498ATP Potential
Motif334 – 3374Involved in interaction with stylet and aphid transmission By similarity
Motif592 – 5943Involved in virions binding and aphid transmission By similarity
Motif1331 – 13344DECH box
Motif1884 – 18929Nuclear localization signal Potential

Sites

Active site1921For P1 proteinase activity By similarity
Active site2011For P1 proteinase activity Potential
Active site2351For P1 proteinase activity By similarity
Active site6261For helper component proteinase activity By similarity
Active site6991For helper component proteinase activity By similarity
Active site20771For nuclear inclusion protein A activity By similarity
Active site21121For nuclear inclusion protein A activity By similarity
Active site21821For nuclear inclusion protein A activity By similarity
Site284 – 2852Cleavage; by P1 proteinase Potential
Site740 – 7412Cleavage; by HC-pro Potential
Site1105 – 11062Cleavage; by NIa-pro By similarity
Site1157 – 11582Cleavage; by NIa-pro By similarity
Site1791 – 17922Cleavage; by NIa-pro By similarity
Site1843 – 18442Cleavage; by NIa-pro By similarity
Site2031 – 20322Cleavage; by NIa-pro By similarity
Site2275 – 22762Cleavage; by NIa-pro By similarity
Site2796 – 27972Cleavage; by NIa-pro By similarity

Amino acid modifications

Modified residue19071O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

Sequence LengthMass (Da)Tools
Isoform Genome polyprotein [UniParc].

Last modified February 1, 1996. Version 2.
Checksum: 3EC79125DE33F1BB

FASTA3,063347,539
        10         20         30         40         50         60 
MATYMSTICF GSFECKLPYS PASCEHIVKE REVPASVDPF ADLETQLSAR LLKQKYATVR 

        70         80         90        100        110        120 
VLKNGTFTYR YKTDAQIMRI QKKLERKDRE EYHFQMAAPS IVSKITIAGG DPPSKSEPQA 

       130        140        150        160        170        180 
PRGIIHTTPR MRKVKTRPII KLTEGQMNHL IKQIKQIMSE KRGSVHLISK KTTHVQYKKI 

       190        200        210        220        230        240 
LGAYSAAVRT AHMMGLRRRV DFRCDMWTVG LLQRLARTDK WSNQVRTINI RRGDSGVILN 

       250        260        270        280        290        300 
TKSLKGHFGR SSGGLFIVRG SHEGKLYDAR SRVTQSILNS MIQFSNADNF WKGLDGNWAR 

       310        320        330        340        350        360 
MRYPSDHTCV AGLPVEDCGR VAALMAHSIL PCYKITCPTC AQQYASLPVS DLFKLLHKHA 

       370        380        390        400        410        420 
RDGLNRLGAD KDRFIHVNKF LIALEHLTEP VDLNLELFNE IFKSIGEKQQ APFKNLNVLN 

       430        440        450        460        470        480 
NFFLKGKENT AHEWQVAQLS LLELARFQKN RTDNIKKGDI SFFRNKLSAK ANWNLYLSCD 

       490        500        510        520        530        540 
NQLDKNANFL WGQREYHAKR FFSNFFEEID PAKGYSAYEI RKHPSGTRKL SIGNLVVPLD 

       550        560        570        580        590        600 
LAEFRQKMKG DYRKQPGVSK KCTSSKDGNY VYPCCCTTLD DGSAIESTFY PPTKKHLVIG 

       610        620        630        640        650        660 
NSGDQKFVDL PKGDSEMLYI AKQGYCYINV FLAMLINISE EDAKDFTKKV RDMCVPKLGT 

       670        680        690        700        710        720 
WPTMMDLATT CAQMRIFYPD VHDAELPRIL VDHDTQTCHV VDSFGSQTTG YHILKASSVS 

       730        740        750        760        770        780 
QLILFANDEL ESDIKHYRVG GVPNASPELG STISPFREGG VIMSESAALK LLLKGIFRPK 

       790        800        810        820        830        840 
VMRQLLLDEP YLLILSILSP GILMAMYNNG IFELAVRLWI NEKQSIAMIA SLLSALALRV 

       850        860        870        880        890        900 
SAAETLVAQR IIIDAAATDL LDATCDGFNL HLTYPTALMV LQVVKNRNEC DDTLFKAGFP 

       910        920        930        940        950        960 
SYNTSVVQIM EKNYLNLLND AWKDLTWREN YPQHGTHTEQ NALSTRYIKP TEKADLKGLY 

       970        980        990       1000       1010       1020 
NISPQAFLGR SAQVVKGTAS GLSERFNNYF NTKCVNISSF FIRRIFRRLP TFVTFVNSLL 

      1030       1040       1050       1060       1070       1080 
VISMLTSVVA VCQAIILDQR KYRREIELMQ IEKNEIVCME LYASLQRKLE RDFTWDEYIE 

      1090       1100       1110       1120       1130       1140 
YLKSVNPQIV QFAQAQMEEY DVRHQRSTPV VKNLEQVVAF MALVIMVFDA ERSDCVFKTL 

      1150       1160       1170       1180       1190       1200 
NKFKGVLSSL DYEVRHQSLD DVIKNFDERN EIIDFELSED TIRTSSVLDT KFSDWWDRQI 

      1210       1220       1230       1240       1250       1260 
QMGHTLPHYR TEGHFMEFTR ATAVQVANDI AHSEHLDFLV RGAVGSGKST GLPVHLSVAG 

      1270       1280       1290       1300       1310       1320 
SVLLIEPTRP LAENVFKQLS SEPFFKKPTL RMRGNSIFGS SPISVMTSGF ALHYFANNRS 

      1330       1340       1350       1360       1370       1380 
QLAQFNFVIF DECHVLDPSA MAFRSLLSVY HQACKVLKVS ATPVGREVEF TTQQPVKLIV 

      1390       1400       1410       1420       1430       1440 
EDTVSFQSFV DAQGSKTNAD VVQFGSNVLV YVSSYNEVDT LAKLLTDKNM MVTKVDGRTM 

      1450       1460       1470       1480       1490       1500 
KHGCLEIVTK GTSARPHFVV ATNIIENGVT LDIDVVVDFG LKVSPFLDID NRSIAYNKVS 

      1510       1520       1530       1540       1550       1560 
VSYGERIQRL GRVGRFKKGV ALRIGHTEKG IIEIPSMVAT EAALACFAYN LPVMTGGVST 

      1570       1580       1590       1600       1610       1620 
SLIGNCTVRQ VKTMQQFELS PFFIQNFVAH DGSMHPVIHD ILKKYKLRDC MTPLCDQSIP 

      1630       1640       1650       1660       1670       1680 
YRASSTWLSV SEYERLGVAL EIPKQVKIAF HIKEIPPKLH EMLWETVVKY KDVCLFPSIR 

      1690       1700       1710       1720       1730       1740 
ASSISKIAYT LRTDLFAIPR TLILVERLLE EERVKQSQFR SLIDEGCSSM FSIVNLTNTL 

      1750       1760       1770       1780       1790       1800 
RARYAKDYTA ENIQKLEKVR SQLKEFSNLD GSACEENLIK RYESLQFVHH QAATSLAKDL 

      1810       1820       1830       1840       1850       1860 
KLKGIWNKSL VAKDLIIAGA VAIGGIGLIY SWFTQSVETV SHQGKNKSKR IQALKFRHAR 

      1870       1880       1890       1900       1910       1920 
DKRAGFEIDN NDDTIEEFFG SAYRKKGKGK GTTVGMGKSS RRFINMYGFD PTEYSFIQFV 

      1930       1940       1950       1960       1970       1980 
DPLTGRQIEE NVYADIRDIQ ERFSEVRKKM VENDDIEMQA LGSNTTIHAY FRKDWCDKAL 

      1990       2000       2010       2020       2030       2040 
KIDLMPHNPL KVCDKTNGIA KFPERELELR QTGPAVEVDV KDIPAQEVEH EAKSLMRGLR 

      2050       2060       2070       2080       2090       2100 
DFNPIAQTVC RLKVSVEYGA SEMYGFGFGA YIVANHHLFR SYNGSMEVQS MHGTFRVKNL 

      2110       2120       2130       2140       2150       2160 
HSLSVLPIKG RDIILIKMPK DFPVFPQKLH FRAPTQNERI CLVGTNFQEK YASSIITETS 

      2170       2180       2190       2200       2210       2220 
TTYNIPGSTF WKHWIETDNG HCGLPVVSTA DGCIVGIHSL ANNAHTTNYY SAFDEDFESK 

      2230       2240       2250       2260       2270       2280 
YLRTNEHNEW VKSWVYNPDT VLWGPLKLKD STPKGLFKTT KLVQDLIDHD VVVEQAKHSA 

      2290       2300       2310       2320       2330       2340 
WMFEALTGNL QAVATMKSQL VTKHVVKGEC RHFTEFLTVD AEAEAEAFFR PLMDAYGKSL 

      2350       2360       2370       2380       2390       2400 
LNRDAYIKDI MKYSKPIDVG VVDRMHLRKP SIGLSSTCNV HGFKKCAYVT DEQEIFKALN 

      2410       2420       2430       2440       2450       2460 
MKAAVGASYG CKKKDYFEHF TDADKEEIVM QSCLRLYKGL LGIWNGSLKA ELRCKEKILA 

      2470       2480       2490       2500       2510       2520 
NKTRTFTAAP LDTLLGGKVC VDDFNNQFYS KNIECCWTVG MTKFYGGWDK LLRRLPENWV 

      2530       2540       2550       2560       2570       2580 
YCDADGSQFD SSLTPYLINA VLTIRSTYME DWDVGLQMLR NLYTEIVYTP ISTPDGTIVK 

      2590       2600       2610       2620       2630       2640 
KFRGNNSGQP STVVDNSLMV VLAMHYALIK ECVEFEEIDS TCVFFVNGDD LLIAVNPEKE 

      2650       2660       2670       2680       2690       2700 
SILDRMSQHF SDLGLNYDFS SRTRRKEELW FMSHRGLLIE GMYVPKLEEE RIVSILQWDR 

      2710       2720       2730       2740       2750       2760 
ADLPEHRLEA ICAAMIESWG YSELTHQIRR FYSWLLQQQP FATIAQEGKA PYIASMALRK 

      2770       2780       2790       2800       2810       2820 
LYMDRAVDEE ELRAFTEMMV ALDDEFELDS YEVHHQANDT IDAGGSNKKD AKPEQGSIQP 

      2830       2840       2850       2860       2870       2880 
NPNKGKDKDV NAGTSGTHTV PRIKAITSKM RMPTSKGATV PNLEHLLEYA PQQIDISNTR 

      2890       2900       2910       2920       2930       2940 
ATQSQFDTWY EAVRMAYDIG ETEMPTVMNG LMVWCIENGT SPNVNGVWVM MDGNEQVEYP 

      2950       2960       2970       2980       2990       3000 
LKPIVENAKP TLRQIMAHFS DVAEAYIEMR NKKEPYMPRY GLIRNLRDMG LARYAFDFYE 

      3010       3020       3030       3040       3050       3060 
VTSRTPVRAR EAHIQMKAAA LKSAQPRLFG LDGGISTQEE NTERHTTEDV SPSMHTLLGV 


KNM 

« Hide

Isoform P3N-PIPO polyprotein [UniParc].

See P0CJ93.

References

[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]"Potyvirus proteins: a wealth of functions."
Urcuqui-Inchima S., Haenni A.L., Bernardi F.
Virus Res. 74:157-175(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X12456 Genomic RNA. Translation: CAA30988.1.
D00441 Genomic RNA. Translation: BAA00342.1.
PIRJS0166.
RefSeqNP_056759.1. NC_001616.1.

3D structure databases

ProteinModelPortalP18247.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSC04.002.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1494052.

Enzyme and pathway databases

BRENDA3.4.22.45. 5005.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR011545. 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]
PfamPF00270. 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]
PRINTSPR00966. NIAPOTYPTASE.
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEPS51192. 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]
ProtoNetSearch...

Entry information

Entry namePOLG_PVYN
AccessionPrimary (citable) accession number: P18247
Secondary accession number(s): Q85266 expand/collapse secondary AC list , Q85267, Q85268, Q85269, Q85270, Q85271, Q85272, Q85273
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: February 1, 1996
Last modified: April 16, 2014
This is version 130 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