Q02963 (POLG_PVYHU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 10 chains: P1 proteinase EC=3.4.-.- Alternative name(s): N-terminal protein Helper component proteinase Short name=HC-pro EC=3.4.22.45 Protein P3 6 kDa protein 1 Short name=6K1 Cytoplasmic inclusion protein Short name=CI EC=3.6.4.- 6 kDa protein 2 Short name=6K2 Viral genome-linked protein Alternative name(s): VPg 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 Nuclear inclusion protein B Short name=NI-b Short name=NIb EC=2.7.7.48 Alternative name(s): RNA-directed RNA polymerase Capsid protein Short name=CP Alternative name(s): Coat protein
Organism	Potato virus Y (strain Hungarian) (PVY) [Complete proteome]
Taxonomic identifier	31739 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Capsicum (peppers) [TaxID: 4071] Solanum lycopersicum (Tomato) (Lycopersicon esculentum) [TaxID: 4081] Nicotiana [TaxID: 4085] Solanum tuberosum (Potato) [TaxID: 4113]

Protein attributes

Sequence length	3061 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	Capsid protein is 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 is a RNA-dependent RNA polymerase that plays an essential role in the virus replication. Helper component proteinase is required for aphid transmission and also has proteolytic activity. 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. 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 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. The viral RNA of potyviruses is expressed as a single polyprotein which undergoes post-translational proteolytic processing by the main proteinase NIa-pro resulting in the production of at least ten 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 potyviruses 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.

Ontologies

Keywords
Biological process	RNA replication
Cellular component	Virion
Ligand	ATP-binding Nucleotide-binding
Molecular function	Capsid protein Helicase Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Suppressor of RNA silencing 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
Cellular component	viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro RNA binding 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 structural molecule 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 – 284	284	P1 proteinase Potential		PRO_0000040397
	Chain	285 – 740	456	Helper component proteinase Potential		PRO_0000040398
	Chain	741 – 1105	365	Protein P3 By similarity		PRO_0000040399
	Chain	1106 – 1157	52	6 kDa protein 1 By similarity		PRO_0000040400
	Chain	1158 – 1791	634	Cytoplasmic inclusion protein By similarity		PRO_0000040401
	Chain	1792 – 1843	52	6 kDa protein 2 By similarity		PRO_0000040402
	Chain	1844 – 2031	188	Viral genome-linked protein By similarity		PRO_0000040403
	Chain	2032 – 2275	244	Nuclear inclusion protein A By similarity		PRO_0000040404
	Chain	2276 – 2794	519	Nuclear inclusion protein B By similarity		PRO_0000040405
	Chain	2795 – 3061	267	Capsid protein By similarity		PRO_0000040406
Regions
	Domain	1229 – 1381	153	Helicase ATP-binding
	Domain	1400 – 1559	160	Helicase C-terminal
	Domain	2032 – 2250	219	Peptidase C4
	Domain	2517 – 2641	125	RdRp catalytic
	Nucleotide binding	1242 – 1249	8	ATP Potential
	Motif	334 – 337	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	592 – 594	3	Involved in virions binding and aphid transmission By similarity
	Motif	1331 – 1334	4	DECH box
	Motif	1884 – 1892	9	Nuclear localization signal Potential
Sites
	Active site	192	1	For P1 proteinase activity By similarity
	Active site	201	1	For P1 proteinase activity Potential
	Active site	235	1	For P1 proteinase activity By similarity
	Active site	626	1	For helper component proteinase activity By similarity
	Active site	699	1	For helper component proteinase activity By similarity
	Active site	2077	1	For nuclear inclusion protein A activity By similarity
	Active site	2112	1	For nuclear inclusion protein A activity By similarity
	Active site	2182	1	For nuclear inclusion protein A activity By similarity
	Site	284 – 285	2	Cleavage; by P1 proteinase Potential
	Site	740 – 741	2	Cleavage; by HC-pro Potential
	Site	1105 – 1106	2	Cleavage; by NIa-pro By similarity
	Site	1157 – 1158	2	Cleavage; by NIa-pro By similarity
	Site	1791 – 1792	2	Cleavage; by NIa-pro By similarity
	Site	1843 – 1844	2	Cleavage; by NIa-pro By similarity
	Site	2031 – 2032	2	Cleavage; by NIa-pro By similarity
	Site	2275 – 2276	2	Cleavage; by NIa-pro By similarity
	Site	2794 – 2795	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1907	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q02963 [UniParc]. Last modified July 1, 1993. Version 1. Checksum: 737FFBA215B56F99	FASTA	3,061	347,330
	10 20 30 40 50 60 MATYTSTIQI GSIECKLPYS PAPFGLVAGK REVSTTTDPF ASLEMQLSAR LRRQEFATIR 70 80 90 100 110 120 TSKNGTCMYR YKTDAQIARI QKKREERERE EYNFQMAASS VVSKITIAGG EPPSKLESQV 130 140 150 160 170 180 RKGVIHTTPR MRTAKTYRTP KLTEGQMNHL IKQVKQIMST KGGSVQLISK KSTHVHYKEV 190 200 210 220 230 240 LGSHRAVVCT AHMRGLRKRV DFRCDKWTVV RLQHLARTDK WTNQVRATDL RKGDSGVILS 250 260 270 280 290 300 NTNLKGHFGR SSEGLFIVRG SHEGKIYDAR SKVTQGVMDS MVQFSSAESF WEGLDGNWAQ 310 320 330 340 350 360 MRYPTDHTCV AGIPVEDCGR VAAIMTHSIL PCYKITCPTC AQQYANLPAS DLLKILHKHA 370 380 390 400 410 420 SDGLNRLGAD KDRFVHVKKF LTILEHLTEP VDLSLEIFNE VFKSIGEKQQ SPFKNLNILN 430 440 450 460 470 480 NFFLKGKENT AREWQVAQLS LLELARFQKN RTDNIKKGDI SFFRNKLSAK ANWNLYLSCD 490 500 510 520 530 540 NQLDKNANFL WGQREYHAKR FFSNYFEEID PAKGYSAYEN RLHPNGTRKL AIGNLIVPLD 550 560 570 580 590 600 LAEFRRKMKG DYKRQPGVSK KCTSSKDGNY VYPCCCTTLD DGSAVESTFY PPTKKHLVIG 610 620 630 640 650 660 NSGDQKYVDL PKGNSEMLYI ARQGFCYINI FLAMLINISE EDAKDFTKKV RDMCVPKLGT 670 680 690 700 710 720 WPTMMDLATT CAQMKIFYPD VHDAELPRIL VDHETQTCHV VDSFGSQTTG YHILKASSVS 730 740 750 760 770 780 QLILFANDEL ESDIKHYRVG GIPNACPELG STISPFREGG VIMSESAALK LLLKGIFRPK 790 800 810 820 830 840 VMRQLLLDEP YLLILSILSP GILMAMYNNG IFELAVKLWI NEKQSIAMIA SLLSALALRV 850 860 870 880 890 900 SAAETLVAQR IIIDTAATDL LDATCDGFNL HLTYPTALMV LQVVKNRNEC DDTLFKAGFP 910 920 930 940 950 960 SYNTSVVQIM EKNYLNLLND AWKDLTWREK LSATWYSYRA KRSITRYIKP TGRADLKGLY 970 980 990 1000 1010 1020 NISPQAFLGR GAQVVKGTAS GLSERFNNYF NTKCVNISSF FIRRIFRRLP TFVTFVNSLL 1030 1040 1050 1060 1070 1080 VISMLTSVVA VCQAIILDQR KYRREIELMQ IEKNEIVCME LYASLQRKLE RDFTWDEYIE 1090 1100 1110 1120 1130 1140 YLKSVNPQIV QFAQAQMEEY DVRHQRSTPG VKNLEQVVAF MALVIMVFDA ERSDCVFKTL 1150 1160 1170 1180 1190 1200 NKFKGVLSSL DHEVRHQSLD DVIKNFDERN ETIDFELSED 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 EDTLSFQSFV DAQGSKTNAD VVQFGSNVLV YVSSYNEVDT LAKLLTDKNM MVTKVDGRTM 1450 1460 1470 1480 1490 1500 KHGCLEIVTR GTSARPHFVV ATNIIENGVT LDIDVVVDFG LKVSPFLDID NRSIAYNKVS 1510 1520 1530 1540 1550 1560 VSYGERIQRL GRVGRFKKGV ALRIGHTEKG IIENPSMIAT 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 KLKGTWKKSL VAKDLIIAGA VAIGGIGLIY SWFTQSVETV SHQGKNKSKR IQALKFRHAR 1870 1880 1890 1900 1910 1920 DKRAGFEIDN NDDTIEEFFG SAYRKKGKGK GTTVGMGKSS RRFVNMYGFD PTEYSFIQFV 1930 1940 1950 1960 1970 1980 DPLTGAQIEE NVYADIRDIQ ERFSDVRKKM VEDDEIELQA LGSNTTIHAY FRKDWSDKAL 1990 2000 2010 2020 2030 2040 KIDLMPHNPL KICDKSNGIA KFPERELELR QTGPAIEVDV KDIPKQEVEH EAKSLMRGLR 2050 2060 2070 2080 2090 2100 DFNPIAQTVC RVKVSAEYGT SEMYGFGFGA YIIVNHHLFK SFNGSMEVRS MHGTFRVKNL 2110 2120 2130 2140 2150 2160 HSLSVLPIKG RDIIIIKMPK DFPVFPQKLH FRAPVQNERI CLVGTNFQEK HASSIITETS 2170 2180 2190 2200 2210 2220 TTYNVPGSTF WKHWIETNDG HCGLPVVSTA DGCLVGIHSL ANNVQTTNYY SAFDEDFESK 2230 2240 2250 2260 2270 2280 YLRTNEHNEW TKSWVYNPDT VLWGPLKLKE STPKGLFKTT KLVQDLIDHD VVVEQAKHSA 2290 2300 2310 2320 2330 2340 WMYEALTGNL QAVATMKSQL VTKHVVKGEC RHFKEFLTVD SEAEAFFRPL MDAYGKSLLN 2350 2360 2370 2380 2390 2400 REAYIKDIMK YSKPIDVGIV DCDAFEEAIN RVIIYLQVHG FQKCNYITDE QEIFKALNMK 2410 2420 2430 2440 2450 2460 AAVGAMYGGK KKDYFEHFTE ADKEEIVMQS CPRLYKGSLG IWNGSLKAEL RCKEKILANK 2470 2480 2490 2500 2510 2520 TRTFTAAPLD TLLGGKVCVD DFNNQFYSKN IECCWTVGMT KFYGGWDRLL RRLPENWVYC 2530 2540 2550 2560 2570 2580 DADGSQFDSS LTPYLINAVL IIRSTYMEDW DLGLQMLRNL YTEIIYTPIS TPDGTIVKKF 2590 2600 2610 2620 2630 2640 RGNNSGQPST VVDNSLMVVL AMHYALIKEC VEFEEIDSTC VFFVNGDDLL IAVNPEKESI 2650 2660 2670 2680 2690 2700 LDRMSQHFSD LGLNYDFSSR TRRKEELWFM SHRGLLIEGM YVPKLEEERI VSILQWDRAD 2710 2720 2730 2740 2750 2760 LPEHRLEAIC AAMIESWGYS ELTHQIRRFY SWLLQQQPFS TIAQEGKAPY IASMALKKLY 2770 2780 2790 2800 2810 2820 MNRTVDEEEL KAFTEMMVAL DDELECDTYE VHHQGNDTID AGGSTKKDAK QEQGSIQPNL 2830 2840 2850 2860 2870 2880 NKEKEKDVNV GTSGTHTVPR IKAITSKMRM PKSKGAAVLN LKHLLEYAPQ QIDISNTRAT 2890 2900 2910 2920 2930 2940 QSQFDTWYEA VQLAYDIGET EMPTVMNGLM VWCIENGTSP NINGVWVMMD GDEQVEYPLK 2950 2960 2970 2980 2990 3000 PIVENAKPTL RQIMAHFSDV AEAYIEMRNK KEPYMPRYGL VRNLRDGSLA RYAFDFYEVT 3010 3020 3030 3040 3050 3060 SRTPVRAREA HIQMKAAALK SAQSRLFGLD GGISTQEENT ERHTTEDVSP SMHTLLGVKN M

References

[1]	"Cloning and sequencing of potato virus Y (Hungarian isolate) genomic RNA." Thole V., Dalmay T., Burgyan J., Balazs E. Gene 123:149-156(1993) [PubMed: 8428653] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Potyvirus proteins: a wealth of functions." Urcuqui-Inchima S., Haenni A.L., Bernardi F. Virus Res. 74:157-175(2001) [PubMed: 11226583] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M95491 Genomic RNA. Translation: AAB59762.1.
PIR	JN0545.
3D structure databases
ProteinModelPortal	Q02963.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR014001. DEAD-like_helicase. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR001650. Helicase_C. IPR009003. Pept_cys/ser_Trypsin-like. IPR002540. Pept_S30_P1_potyvir. IPR001730. Peptidase_C4. IPR001456. Peptidase_C6. IPR001592. Poty_coat. IPR013648. PP_Potyviridae. IPR001205. RNA-dir_pol_picornavirus. IPR007094. RNA-dir_pol_PSvirus. [Graphical view]
Pfam	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]
PRINTS	PR00966. NIAPOTYPTASE.
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	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]
ProtoNet	Search...

Entry information

Entry name

POLG_PVYHU

Accession

Primary (citable) accession number: Q02963

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 1, 1993
Last modified:	November 16, 2011
This is version 103 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program