Q6XW15 (POLG_BTMV) 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	Beet mosaic virus (BtMV) [Complete proteome]
Taxonomic identifier	114921 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Amaranthus retroflexus (Redroot amaranth) (Redroot pigweed) [TaxID: 124763] Beta vulgaris subsp. maritima (Sea beet) (Beta maritima) [TaxID: 350892] Beta vulgaris subsp. vulgaris [TaxID: 3555] Chenopodium album (Lamb's-quarters) [TaxID: 3559] Melilotus indicus (Sourclover) (Yellow sweet clover) [TaxID: 200951] Sonchus arvensis (Perennial sowthistle) [TaxID: 50192] Spinacia oleracea (Spinach) [TaxID: 3562] Trifolium incarnatum (Crimson clover) [TaxID: 60916]

Protein attributes

Sequence length	3085 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: 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: a 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. Cytoplasmic inclusion protein: has helicase activity. It may be involved in replication By similarity. 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. Genome polyprotein of potyviruses 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 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.

Ontologies

Keywords
Biological process	Viral RNA replication
Cellular component	Virion
Coding sequence diversity	Ribosomal frameshifting
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...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Isoform Genome polyprotein (identifier: Q6XW15-1)

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: P0CJ96-1)

The sequence of this isoform can be found in the external entry P0CJ96.
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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 3085	3085	Genome polyprotein		PRO_0000419994
	Chain	1 – 313	313	P1 proteinase Potential		PRO_0000040246
	Chain	314 – 770	457	Helper component proteinase Potential		PRO_0000040247
	Chain	771 – 1117	347	Protein P3 Potential		PRO_0000040248
	Chain	1118 – 1169	52	6 kDa protein 1 By similarity		PRO_0000040249
	Chain	1170 – 1803	634	Cytoplasmic inclusion protein By similarity		PRO_0000040250
	Chain	1804 – 1855	52	6 kDa protein 2 By similarity		PRO_0000040251
	Chain	1856 – 2046	191	Viral genome-linked protein By similarity		PRO_0000040252
	Chain	2047 – 2293	247	Nuclear inclusion protein A By similarity		PRO_0000040253
	Chain	2294 – 2809	516	Nuclear inclusion protein B By similarity		PRO_0000040254
	Chain	2810 – 3085	276	Capsid protein		PRO_0000040255
Regions
	Domain	1241 – 1393	153	Helicase ATP-binding
	Domain	1412 – 1571	160	Helicase C-terminal
	Domain	2047 – 2266	220	Peptidase C4
	Domain	2535 – 2659	125	RdRp catalytic
	Nucleotide binding	1254 – 1261	8	ATP Potential
	Motif	365 – 368	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	622 – 624	3	Involved in virions binding and aphid transmission By similarity
	Motif	1343 – 1346	4	DESH box
	Motif	1895 – 1904	10	Nuclear localization signal Potential
Sites
	Active site	656	1	For helper component proteinase activity By similarity
	Active site	729	1	For helper component proteinase activity By similarity
	Active site	2092	1	For nuclear inclusion protein A activity By similarity
	Active site	2127	1	For nuclear inclusion protein A activity By similarity
	Active site	2198	1	For nuclear inclusion protein A activity By similarity
	Site	313 – 314	2	Cleavage; by P1 proteinase Potential
	Site	770 – 771	2	Cleavage; by HC-pro Potential
	Site	1117 – 1118	2	Cleavage; by NIa-pro By similarity
	Site	1169 – 1170	2	Cleavage; by NIa-pro By similarity
	Site	1803 – 1804	2	Cleavage; by NIa-pro By similarity
	Site	1855 – 1856	2	Cleavage; by NIa-pro By similarity
	Site	2046 – 2047	2	Cleavage; by NIa-pro By similarity
	Site	2293 – 2294	2	Cleavage; by NIa-pro By similarity
	Site	2809 – 2810	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1919	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Isoform Genome polyprotein [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 918576B242794C0D	FASTA	3,085	349,731
	10 20 30 40 50 60 MATMMHFGQF PSNIPLRAAT CCTKVHSTLV TKEMMASSVK PAESSSVARP IIYSSAATDG 70 80 90 100 110 120 YEKAQRAFEA SFREKYSGKL EAMKYGKMVK KGGLTYVKRA GPQAIAKGIE MDAAIEKFNT 130 140 150 160 170 180 AFNAGELENV TLEGDITAGI SVARGESVWL RSVFWSRSLK KQARKKTPKL VAKSDFDDLF 190 200 210 220 230 240 NKVLKVASLG NIPVEIVGKK ANKILRCGYR RVNTSTIPYF HLPHHNSNYI CRELHPQRVR 250 260 270 280 290 300 WLVPLLVRHR KIRDQFSDSM IARGWSGLIL PKYIASTCGR RYDEVIVRGR LYGRVEDART 310 320 330 340 350 360 KLPAGDVGRT MHYSSGEERF FAGWKEGFEK LVPAQKEHIC KIVQDNKFCG KLAASIVQIA 370 380 390 400 410 420 FPCHKMACDV CRNKFNEMTP EAYSELIDKH IDQRMNEINE AIVRFPGLKQ VVSNFRSKHI 430 440 450 460 470 480 ASTNIKDNLE VAKLTQGHKA NQMMQLARIN SILIKGNTAT PSEISDASGL LLEITRWFNN 490 500 510 520 530 540 HLSVIDKGSL RAFRNKRSSK ALVNPSLLCD NQRDKNGNFI WGERGYHSKR FFASHFDEVT 550 560 570 580 590 600 PGDGYKEYII RKGPQGQRKL AIGNLIVSFD LEKTRQALKG EEVEKLPLSN SCVSKRNGNY 610 620 630 640 650 660 VYTSCCVTLD DGTPLYSNIK NPTKRHLVVG TTGDPKIVDL PATDTDKMYI AKEGYCYLNI 670 680 690 700 710 720 FLAMLINVNE NEAKAFTKMV RDIIIPMLGT WPTMQDLATA CFMMTAFFPE TSSAELPRIL 730 740 750 760 770 780 VDHTNQTMHV IDSFGSLTTG YHVLKAGTAA QLIDFASTEL EGEMKWYRVG GHGLPVKEKM 790 800 810 820 830 840 ISALITSIFR PKKLVYLIEE DPYVLIMAMC SPRLIISLFN NGALELAAKH WISRDKNVSA 850 860 870 880 890 900 IFAMLMDLST EMSKAELLIE QHRMINECAK RVHDTQNYLD EVGPHQQEVR TFLALISDEL 910 920 930 940 950 960 EADKELHKTG FANFSERFHS LTEKMYVDAL EEEWRGLSLL DRFSYATFVY KHKPRSTSVL 970 980 990 1000 1010 1020 PPKKSEDIDA KFVISPSWFV GKTKEHLSGG RKYVTSQITQ FTSYIKRATL DRAMRIMCSC 1030 1040 1050 1060 1070 1080 LKDLAYFMNV ALVTHLLISM IAAVYNMLND HRIAKRRLYI LEMQETNTAI WHLYDTWKTV 1090 1100 1110 1120 1130 1140 NQRDPTHEEF RKYVAKVNKN LLRHLPEEED KAEVEYQANK VYEKKLEKAV ALMALFTMIF 1150 1160 1170 1180 1190 1200 DTEKSGAVFS ILRNIKSVFS TLGEEVKYQS LDEIQSIEDE KKLTIDFDLD TEITAEHTTM 1210 1220 1230 1240 1250 1260 DVQFEKWWDK QLSQNRVVPH YRVGGTFIEF TRHTAASVCN TICASSEQEF VVRGAVGSGK 1270 1280 1290 1300 1310 1320 STGLPSHLSR KGRVLLLEPT RPLAENVCKQ LRKEPFHLSP TLRMRGLTTF GSSNISVMTS 1330 1340 1350 1360 1370 1380 GYALHFHANN PQRLEEFDFI MIDESHTMDS STMAFYCLLR EYEFKGKILK VSATPPGREC 1390 1400 1410 1420 1430 1440 EFKTQHDVLI KIEESLSYNS FVTAQGTGSN ADVVQNGDNI LVYVPSYNDV DQLSKGLMEK 1450 1460 1470 1480 1490 1500 GHLVTKVDGR TMKMGNVEIP TKGTSSKKHF IVATNIIENG VTLDIDVVVD FGLKVVAELD 1510 1520 1530 1540 1550 1560 SDSRCMRYKK VSISYGERLQ RLGRVGRVKQ GTALRIGHTE TGMTEIPVAI ATEAAFICFA 1570 1580 1590 1600 1610 1620 YNLPVMTHNV TSSLLSRCTN RQARTMMQYE LSPFFMVELV HFNGCVHPQI ESKLKAYKLR 1630 1640 1650 1660 1670 1680 DSETQLSTLA IPNSGTSRWK TVGEYKKLGV RIEADDNVRV PFAANGVPDR LYADLWETIQ 1690 1700 1710 1720 1730 1740 QHKSDAGFGR LTSACASKIS YTLTTQPNAI PRTLAIIEHL LREEQQKKAY FESLNDTLCA 1750 1760 1770 1780 1790 1800 TSFSLAGMVN NIRRRYLKDH SAHNINVLQN AKSQLNEFNS KAIDPERVGD IMGYGVLDTV 1810 1820 1830 1840 1850 1860 QYQSATDVQK RLKLKGRWNG SLAATDLLIA GAVFAGGCWM LWEYTKSGNE IVQYQGKRRQ 1870 1880 1890 1900 1910 1920 MQKLKFRNAR DNKVGREVYG DDGTIEHFFG AAYTERGKRK GNNSTKGMGT KTRRFVHMYG 1930 1940 1950 1960 1970 1980 FDPTEYSFVR FVDPLTGYSK DESVQTDISL VQSEIGEYRQ KCMEDDDELI DFIKQKPGIQ 1990 2000 2010 2020 2030 2040 AYFMKNGSDK ALQVDLTPHI PLLSCAKTAT IAGFPERESE LRQTGTPIVV NKNVVPGEHK 2050 2060 2070 2080 2090 2100 EVVREEGKSI VKGLRNYNPI SSVVCRLTND SNGNAQTLYG VGFGPLIITN SHLFKMNNGT 2110 2120 2130 2140 2150 2160 LFVRSHQGEF TVQNTTQLQI YHVKDKDMIL IRMPKDFPPF PMKLKFRAPH SEERACLVGS 2170 2180 2190 2200 2210 2220 RFQQKSLSSE VSDSTLIRPT DSGSGYWKHW VSTKEGDCGL PMVALKDGSL IGIHGLTSVR 2230 2240 2250 2260 2270 2280 SELNYFVPFT DDFQSKYLSN IESLEWVKHW RHTPDKVAWN GMTLRENGPA SEFSVSKLIA 2290 2300 2310 2320 2330 2340 DLTHGYVDEV VEQGYSSKWV ANRLDGNLKA VASSSSQLVT KHVVKGPCVL FQEFLATHEE 2350 2360 2370 2380 2390 2400 AARYFVPRMG EYGPSRLNKE AFLKDFLKYA GPITVGVVNT NSFEDAVASV INMLEDLDYG 2410 2420 2430 2440 2450 2460 ECAYVTDPDS IFDSLNMKAA VGALYKGKKK EYFEQLNTTE REDLLRLSCE RLYEGKMGVW 2470 2480 2490 2500 2510 2520 NGSLKAELRP KEKLEQNKTR TFTAAPIDTL LGGKVCVDDF NNRFYSLNLK GPWSVGMTKF 2530 2540 2550 2560 2570 2580 YGGWNELLQK LPDGWIYCDA DGSQFDSSLT PYLINAVVQI REHFMEDWEI GRTMLRNFYT 2590 2600 2610 2620 2630 2640 EIVYTPILTP DGTIVKKFKG NNSGQPSTVV DNTLMVILAM HYAMHQQCWK EEEMKEKIRF 2650 2660 2670 2680 2690 2700 FANGDDLLIA IYPSKEKFLN VLSEYFHELG LKYDFSSRST VRETLWFMSH RGLYLDDMYI 2710 2720 2730 2740 2750 2760 PKLEEERIVS ILEWDRSNEA THRAEAICAA MIEAWGYPEL LKYIREFYLW MMQHECYRDL 2770 2780 2790 2800 2810 2820 VRDGKLPYIA ETALRKLYTD KSVDENELVK YWKALAPEED DGPDIVTYQG DEKPSKSSQP 2830 2840 2850 2860 2870 2880 QSSSPQVPQQ VDAGASSQGR DKQSVIKHDS TKSKDVGQSS TAVPRLKQIS KMRMPVSKGR 2890 2900 2910 2920 2930 2940 QVLALDHLLD YKPEQVDLSN TRATKEQFDN WYEAVMREYD VSDSQMGVIM NGLMVWCIEN 2950 2960 2970 2980 2990 3000 GTSPNLSGDW VMMDGEEQVS FPLKPIVENA KPSFRQIMHH FSDAAEAYIE MRNRERPYMP 3010 3020 3030 3040 3050 3060 RYGAQRNLRD KTLARYAFDF YEVTSRTTDR AREAHFQMKA AALASVSNKL FGLDGSVATT 3070 3080 SEDTERHTAT DVNAHMHHMM GVRQG
	Isoform P3N-PIPO polyprotein [UniParc]. See P0CJ96.		–	–

References

[1]	"The complete nucleotide sequence, genome organization, and specific detection of beet mosaic virus." Nemchinov L.G., Hammond J., Jordan R., Hammond R.W. Arch. Virol. 149:1201-1214(2004) [PubMed] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY206394 Genomic RNA. Translation: AAP41071.1.
RefSeq	NP_954611.1. NC_005304.1.
3D structure databases
ProteinModelPortal	Q6XW15.
SMR	Q6XW15. Positions 2055-2269.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. 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]
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_BTMV

Accession

Primary (citable) accession number: Q6XW15

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2005
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program