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Protein

Genome polyprotein

Gene
N/A
Organism
Potato virus Y (strain Hungarian) (PVY)
Status
Reviewed-Annotation score: 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.
Nuclear inclusion protein B: an RNA-dependent RNA polymerase that plays an essential role in the virus replication.
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 (By similarity).By similarity
Cytoplasmic inclusion protein: has helicase activity. It may be involved in replication.
Both 6K peptides are indispensable for virus replication.By similarity
Nuclear inclusion protein A: has RNA-binding and proteolytic activities.

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).PROSITE-ProRule annotation
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)DescriptionActionsGraphical viewLength
Active sitei192For P1 proteinase activityBy similarity1
Active sitei201For P1 proteinase activitySequence analysis1
Active sitei235For P1 proteinase activityBy similarity1
Active sitei626For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei699For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei2077For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2112For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2182For nuclear inclusion protein A activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1242 – 1249ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

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

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 Hungarian) (PVY)
Taxonomic identifieri31739 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA 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]
Proteomesi
  • UP000008616 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Helical capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004200161 – 3061Genome polyproteinAdd BLAST3061
ChainiPRO_00000403971 – 284P1 proteinaseSequence analysisAdd BLAST284
ChainiPRO_0000040398285 – 740Helper component proteinaseSequence analysisAdd BLAST456
ChainiPRO_0000040399741 – 1105Protein P3By similarityAdd BLAST365
ChainiPRO_00000404001106 – 11576 kDa protein 1By similarityAdd BLAST52
ChainiPRO_00000404011158 – 1791Cytoplasmic inclusion proteinBy similarityAdd BLAST634
ChainiPRO_00000404021792 – 18436 kDa protein 2By similarityAdd BLAST52
ChainiPRO_00000404031844 – 2031Viral genome-linked proteinBy similarityAdd BLAST188
ChainiPRO_00000404042032 – 2275Nuclear inclusion protein ABy similarityAdd BLAST244
ChainiPRO_00000404052276 – 2794Nuclear inclusion protein BBy similarityAdd BLAST519
ChainiPRO_00000404062795 – 3061Capsid proteinBy similarityAdd BLAST267

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1907O-(5'-phospho-RNA)-tyrosineBy similarity1

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).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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei284 – 285Cleavage; by P1 proteinaseSequence analysis2
Sitei740 – 741Cleavage; by autolysisPROSITE-ProRule annotation2
Sitei1105 – 1106Cleavage; by NIa-proBy similarity2
Sitei1157 – 1158Cleavage; by NIa-proBy similarity2
Sitei1791 – 1792Cleavage; by NIa-proBy similarity2
Sitei1843 – 1844Cleavage; by NIa-proBy similarity2
Sitei2031 – 2032Cleavage; by NIa-proBy similarity2
Sitei2275 – 2276Cleavage; by NIa-proBy similarity2
Sitei2794 – 2795Cleavage; by NIa-proBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Structurei

3D structure databases

ProteinModelPortaliQ02963.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini618 – 740Peptidase C6PROSITE-ProRule annotationAdd BLAST123
Domaini1229 – 1381Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST153
Domaini1400 – 1559Helicase C-terminalPROSITE-ProRule annotationAdd BLAST160
Domaini2032 – 2250Peptidase C4PROSITE-ProRule annotationAdd BLAST219
Domaini2517 – 2641RdRp catalyticPROSITE-ProRule annotationAdd BLAST125

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi334 – 337Involved in interaction with stylet and aphid transmissionBy similarity4
Motifi592 – 594Involved in virions binding and aphid transmissionBy similarity3
Motifi1331 – 1334DECH box4
Motifi1884 – 1892Nuclear localization signalSequence analysis9

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

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 peptidase C4 domain.PROSITE-ProRule annotation
Contains 1 peptidase C6 domain.PROSITE-ProRule annotationCurated
Contains 1 peptidase S30 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR001456. HC-pro.
IPR031159. HC_PRO_CPD_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR009003. Peptidase_S1_PA.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[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.
PROSITEiPS51744. HC_PRO_CPD. 1 hit.
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]

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. AlignAdd to basket

Isoform Genome polyprotein (identifier: Q02963-1) [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.

« Hide

        10         20         30         40         50
MATYTSTIQI GSIECKLPYS PAPFGLVAGK REVSTTTDPF ASLEMQLSAR
60 70 80 90 100
LRRQEFATIR TSKNGTCMYR YKTDAQIARI QKKREERERE EYNFQMAASS
110 120 130 140 150
VVSKITIAGG EPPSKLESQV RKGVIHTTPR MRTAKTYRTP KLTEGQMNHL
160 170 180 190 200
IKQVKQIMST KGGSVQLISK KSTHVHYKEV LGSHRAVVCT AHMRGLRKRV
210 220 230 240 250
DFRCDKWTVV RLQHLARTDK WTNQVRATDL RKGDSGVILS NTNLKGHFGR
260 270 280 290 300
SSEGLFIVRG SHEGKIYDAR SKVTQGVMDS MVQFSSAESF WEGLDGNWAQ
310 320 330 340 350
MRYPTDHTCV AGIPVEDCGR VAAIMTHSIL PCYKITCPTC AQQYANLPAS
360 370 380 390 400
DLLKILHKHA SDGLNRLGAD KDRFVHVKKF LTILEHLTEP VDLSLEIFNE
410 420 430 440 450
VFKSIGEKQQ SPFKNLNILN NFFLKGKENT AREWQVAQLS LLELARFQKN
460 470 480 490 500
RTDNIKKGDI SFFRNKLSAK ANWNLYLSCD NQLDKNANFL WGQREYHAKR
510 520 530 540 550
FFSNYFEEID PAKGYSAYEN RLHPNGTRKL AIGNLIVPLD LAEFRRKMKG
560 570 580 590 600
DYKRQPGVSK KCTSSKDGNY VYPCCCTTLD DGSAVESTFY PPTKKHLVIG
610 620 630 640 650
NSGDQKYVDL PKGNSEMLYI ARQGFCYINI FLAMLINISE EDAKDFTKKV
660 670 680 690 700
RDMCVPKLGT WPTMMDLATT CAQMKIFYPD VHDAELPRIL VDHETQTCHV
710 720 730 740 750
VDSFGSQTTG YHILKASSVS QLILFANDEL ESDIKHYRVG GIPNACPELG
760 770 780 790 800
STISPFREGG VIMSESAALK LLLKGIFRPK VMRQLLLDEP YLLILSILSP
810 820 830 840 850
GILMAMYNNG IFELAVKLWI NEKQSIAMIA SLLSALALRV SAAETLVAQR
860 870 880 890 900
IIIDTAATDL LDATCDGFNL HLTYPTALMV LQVVKNRNEC DDTLFKAGFP
910 920 930 940 950
SYNTSVVQIM EKNYLNLLND AWKDLTWREK LSATWYSYRA KRSITRYIKP
960 970 980 990 1000
TGRADLKGLY NISPQAFLGR GAQVVKGTAS GLSERFNNYF NTKCVNISSF
1010 1020 1030 1040 1050
FIRRIFRRLP TFVTFVNSLL VISMLTSVVA VCQAIILDQR KYRREIELMQ
1060 1070 1080 1090 1100
IEKNEIVCME LYASLQRKLE RDFTWDEYIE YLKSVNPQIV QFAQAQMEEY
1110 1120 1130 1140 1150
DVRHQRSTPG VKNLEQVVAF MALVIMVFDA ERSDCVFKTL NKFKGVLSSL
1160 1170 1180 1190 1200
DHEVRHQSLD DVIKNFDERN ETIDFELSED TIRTSSVLDT KFSDWWDRQI
1210 1220 1230 1240 1250
QMGHTLPHYR TEGHFMEFTR ATAVQVANDI AHSEHLDFLV RGAVGSGKST
1260 1270 1280 1290 1300
GLPVHLSVAG SVLLIEPTRP LAENVFKQLS SEPFFKKPTL RMRGNSIFGS
1310 1320 1330 1340 1350
SPISVMTSGF ALHYFANNRS QLAQFNFVIF DECHVLDPSA MAFRSLLSVY
1360 1370 1380 1390 1400
HQACKVLKVS ATPVGREVEF TTQQPVKLIV EDTLSFQSFV DAQGSKTNAD
1410 1420 1430 1440 1450
VVQFGSNVLV YVSSYNEVDT LAKLLTDKNM MVTKVDGRTM KHGCLEIVTR
1460 1470 1480 1490 1500
GTSARPHFVV ATNIIENGVT LDIDVVVDFG LKVSPFLDID NRSIAYNKVS
1510 1520 1530 1540 1550
VSYGERIQRL GRVGRFKKGV ALRIGHTEKG IIENPSMIAT EAALACFAYN
1560 1570 1580 1590 1600
LPVMTGGVST SLIGNCTVRQ VKTMQQFELS PFFIQNFVAH DGSMHPVIHD
1610 1620 1630 1640 1650
ILKKYKLRDC MTPLCDQSIP YRASSTWLSV SEYERLGVAL EIPKQVKIAF
1660 1670 1680 1690 1700
HIKEIPPKLH EMLWETVVKY KDVCLFPSIR ASSISKIAYT LRTDLFAIPR
1710 1720 1730 1740 1750
TLILVERLLE EERVKQSQFR SLIDEGCSSM FSIVNLTNTL RARYAKDYTA
1760 1770 1780 1790 1800
ENIQKLEKVR SQLKEFSNLD GSACEENLIK RYESLQFVHH QAATSLAKDL
1810 1820 1830 1840 1850
KLKGTWKKSL VAKDLIIAGA VAIGGIGLIY SWFTQSVETV SHQGKNKSKR
1860 1870 1880 1890 1900
IQALKFRHAR DKRAGFEIDN NDDTIEEFFG SAYRKKGKGK GTTVGMGKSS
1910 1920 1930 1940 1950
RRFVNMYGFD PTEYSFIQFV DPLTGAQIEE NVYADIRDIQ ERFSDVRKKM
1960 1970 1980 1990 2000
VEDDEIELQA LGSNTTIHAY FRKDWSDKAL KIDLMPHNPL KICDKSNGIA
2010 2020 2030 2040 2050
KFPERELELR QTGPAIEVDV KDIPKQEVEH EAKSLMRGLR DFNPIAQTVC
2060 2070 2080 2090 2100
RVKVSAEYGT SEMYGFGFGA YIIVNHHLFK SFNGSMEVRS MHGTFRVKNL
2110 2120 2130 2140 2150
HSLSVLPIKG RDIIIIKMPK DFPVFPQKLH FRAPVQNERI CLVGTNFQEK
2160 2170 2180 2190 2200
HASSIITETS TTYNVPGSTF WKHWIETNDG HCGLPVVSTA DGCLVGIHSL
2210 2220 2230 2240 2250
ANNVQTTNYY SAFDEDFESK YLRTNEHNEW TKSWVYNPDT VLWGPLKLKE
2260 2270 2280 2290 2300
STPKGLFKTT KLVQDLIDHD VVVEQAKHSA WMYEALTGNL QAVATMKSQL
2310 2320 2330 2340 2350
VTKHVVKGEC RHFKEFLTVD SEAEAFFRPL MDAYGKSLLN REAYIKDIMK
2360 2370 2380 2390 2400
YSKPIDVGIV DCDAFEEAIN RVIIYLQVHG FQKCNYITDE QEIFKALNMK
2410 2420 2430 2440 2450
AAVGAMYGGK KKDYFEHFTE ADKEEIVMQS CPRLYKGSLG IWNGSLKAEL
2460 2470 2480 2490 2500
RCKEKILANK TRTFTAAPLD TLLGGKVCVD DFNNQFYSKN IECCWTVGMT
2510 2520 2530 2540 2550
KFYGGWDRLL RRLPENWVYC DADGSQFDSS LTPYLINAVL IIRSTYMEDW
2560 2570 2580 2590 2600
DLGLQMLRNL YTEIIYTPIS TPDGTIVKKF RGNNSGQPST VVDNSLMVVL
2610 2620 2630 2640 2650
AMHYALIKEC VEFEEIDSTC VFFVNGDDLL IAVNPEKESI LDRMSQHFSD
2660 2670 2680 2690 2700
LGLNYDFSSR TRRKEELWFM SHRGLLIEGM YVPKLEEERI VSILQWDRAD
2710 2720 2730 2740 2750
LPEHRLEAIC AAMIESWGYS ELTHQIRRFY SWLLQQQPFS TIAQEGKAPY
2760 2770 2780 2790 2800
IASMALKKLY MNRTVDEEEL KAFTEMMVAL DDELECDTYE VHHQGNDTID
2810 2820 2830 2840 2850
AGGSTKKDAK QEQGSIQPNL NKEKEKDVNV GTSGTHTVPR IKAITSKMRM
2860 2870 2880 2890 2900
PKSKGAAVLN LKHLLEYAPQ QIDISNTRAT QSQFDTWYEA VQLAYDIGET
2910 2920 2930 2940 2950
EMPTVMNGLM VWCIENGTSP NINGVWVMMD GDEQVEYPLK PIVENAKPTL
2960 2970 2980 2990 3000
RQIMAHFSDV AEAYIEMRNK KEPYMPRYGL VRNLRDGSLA RYAFDFYEVT
3010 3020 3030 3040 3050
SRTPVRAREA HIQMKAAALK SAQSRLFGLD GGISTQEENT ERHTTEDVSP
3060
SMHTLLGVKN M
Note: Produced by conventional translation.
Length:3,061
Mass (Da):347,330
Last modified:July 1, 1993 - v1
Checksum:i737FFBA215B56F99
GO
Isoform P3N-PIPO polyprotein (identifier: P0CK06-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0CK06.
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):111,327
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95491 Genomic RNA. Translation: AAB59762.1.
PIRiJN0545.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95491 Genomic RNA. Translation: AAB59762.1.
PIRiJN0545.

3D structure databases

ProteinModelPortaliQ02963.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR001456. HC-pro.
IPR031159. HC_PRO_CPD_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR009003. Peptidase_S1_PA.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[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.
PROSITEiPS51744. HC_PRO_CPD. 1 hit.
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]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_PVYHU
AccessioniPrimary (citable) accession number: Q02963
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: September 16, 2015
This is version 126 of the entry and version 1 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.