P09814 (POLG_TVMV) 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	Tobacco vein mottling virus (TVMV) [Complete proteome]
Taxonomic identifier	12228 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Nicotiana tabacum (Common tobacco) [TaxID: 4097] Rumex [TaxID: 3618]

Protein attributes

Sequence length	3023 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

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. 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. 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.

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 Direct protein sequencing
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: P09814-1)

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: P0CK10-1)

The sequence of this isoform can be found in the external entry P0CK10.
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 – 3023	3023	Genome polyprotein		PRO_0000420031
	Chain	1 – 274	274	P1 proteinase Potential		PRO_0000040483
	Chain	275 – 731	457	Helper component proteinase Potential		PRO_0000040484
	Chain	732 – 1078	347	Protein P3 By similarity		PRO_0000040485
	Chain	1079 – 1130	52	6 kDa protein 1 By similarity		PRO_0000040486
	Chain	1131 – 1765	635	Cytoplasmic inclusion protein By similarity		PRO_0000040487
	Chain	1766 – 1818	53	6 kDa protein 2 By similarity		PRO_0000040488
	Chain	1819 – 2001	183	Viral genome-linked protein By similarity		PRO_0000040489
	Chain	2002 – 2242	241	Nuclear inclusion protein A By similarity		PRO_0000040490
	Chain	2243 – 2758	516	Nuclear inclusion protein B By similarity		PRO_0000040491
	Chain	2759 – 3023	265	Capsid protein By similarity		PRO_0000040492
Regions
	Domain	1202 – 1354	153	Helicase ATP-binding
	Domain	1367 – 1532	166	Helicase C-terminal
	Domain	2002 – 2218	217	Peptidase C4
	Domain	2484 – 2608	125	RdRp catalytic
	Nucleotide binding	1215 – 1222	8	ATP Potential
	Motif	325 – 328	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	583 – 585	3	Involved in virions binding and aphid transmission By similarity
	Motif	1304 – 1307	4	DEFH box
	Motif	1856 – 1863	8	Nuclear localization signal Potential
Sites
	Active site	183	1	For P1 proteinase activity By similarity
	Active site	192	1	For P1 proteinase activity Potential
	Active site	225	1	For P1 proteinase activity By similarity
	Active site	617	1	For helper component proteinase activity By similarity
	Active site	690	1	For helper component proteinase activity By similarity
	Active site	2047	1	For nuclear inclusion protein A activity By similarity
	Active site	2082	1	For nuclear inclusion protein A activity By similarity
	Active site	2152	1	For nuclear inclusion protein A activity By similarity
	Site	274 – 275	2	Cleavage; by P1 proteinase Potential
	Site	731 – 732	2	Cleavage; by HC-pro Potential
	Site	1078 – 1079	2	Cleavage; by NIa-pro By similarity
	Site	1130 – 1131	2	Cleavage; by NIa-pro By similarity
	Site	1765 – 1766	2	Cleavage; by NIa-pro By similarity
	Site	1818 – 1819	2	Cleavage; by NIa-pro By similarity
	Site	2001 – 2002	2	Cleavage; by NIa-pro By similarity
	Site	2242 – 2243	2	Cleavage; by NIa-pro By similarity
	Site	2758 – 2759	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1878	1	O-(5'-phospho-RNA)-tyrosine

Sequences

	Sequence		Length	Mass (Da)
	Isoform Genome polyprotein [UniParc]. Last modified May 30, 2000. Version 2. Checksum: 299FDED15C0E5B87	FASTA	3,023	342,285
	10 20 30 40 50 60 MAATMIFGSF THDLLGKAMS TIHSAVTAEK DIFSSIKERL ERKRHGKICR MKNGSIYIKA 70 80 90 100 110 120 ASSTKVEKIN AAAKKLADDK AAFLKAQPTI VDKIIVNEKI QVVEAEEVHK REDVQTVFFK 130 140 150 160 170 180 KTKKRAPKLR ATCSSSGLDN LYNAVANIAK ASSLRVEVIH KKRVCGEFKQ TRFGRALFID 190 200 210 220 230 240 VAHAKGHRRR IDCRMHRREQ RTMHMFMRKT TKTEVRSKHL RKGDSGIVLL TQKIKGHLSG 250 260 270 280 290 300 VRDEFFIVRG TCDDSLLEAR ARFSQSITLR ATHFSTGDIF WKGFNASFQE QKAIGLDHTC 310 320 330 340 350 360 TSDLPVEACG HVAALMCQSL FPCGKITCKR CIANLSNLDF DTFSELQGDR AMRILDVMRA 370 380 390 400 410 420 RFPSFTHTIR FLHDLFTQRR VTNPNTAAFR EILRLIGDRN EAPFAHVNRL NEILLLGSKA 430 440 450 460 470 480 NPDSLAKASD SLLELARYLN NRTENIRNGS LKHFRNKISS KAHSNLALSC DNQLDQNGNF 490 500 510 520 530 540 LWGLAGIAAK RFLNNYFETI DPEQGYDKYV IRKNPNGERK LAIGNFIIST NLEKLRDQLE 550 560 570 580 590 600 GESIARVGIT EECVSRKDGN YRYPCCCVTL EDGSPMYSEL KMPTKNHLVI GNSGDPKYLD 610 620 630 640 650 660 LPGEISNLMY IAKEGYCYIN IFLAMLVNVD EANAKDFTKR VRDESVQKLG KWPSLIDVAT 670 680 690 700 710 720 ECALLSTYYP AAASAELPRL LVDHAQKTIH VVDSYGSLNT GYHILKANTV SQLEKFASNT 730 740 750 760 770 780 LESPMAQYKV GGLVYSENND ASAVKALTQA IFRPDVLSEL IEKEPYLMVF ALVSPGILMA 790 800 810 820 830 840 MSNSGALEFG ISKWISSDHS LVRMASILKT LASKVSVADT LALQKHIMRQ NANFLCGELI 850 860 870 880 890 900 NGFQKKKSYT HATRFLLMIS EENEMDDPVL NAGYRVLEAS SHEIMEKTYL ALLETSWSDL 910 920 930 940 950 960 SLYGKFKSIW FTRKHFGRYK AELFPKEQTD LQGRYSNSLR FHYQSTLKRL RNKGSLCRER 970 980 990 1000 1010 1020 FLESISSARR RTTCAVFSLL HKAFPDVLKF INTLVIVSLS MQIYYMLVAI IHEHRAAKIK 1030 1040 1050 1060 1070 1080 SAQLEERVLE DKTMLLYDDF KAKLPEGSFE EFLEYTRQRD KEVYEYLMME TTEIVEFQAK 1090 1100 1110 1120 1130 1140 NTGQASLERI IAFVSLTLML FDNERSDCVY KILTKFKGIL GSVENNVRFQ SLDTIVPTQE 1150 1160 1170 1180 1190 1200 EKNMVIDFEL DSDTAHTPQM QEQTFSDWWS NQIANNRVVP HYRTEGYFMQ FTRNTASAVS 1210 1220 1230 1240 1250 1260 HQIAHNEHKD IILMGAVGSG KSTGLPTNLC KFGGVLLLEP TRPLAENVTK QMRGSPFFAS 1270 1280 1290 1300 1310 1320 PTLRMRNLST FGSSPITVMT TGFALHFFAN NVKEFDRYQF IIFDEFHVLD SNAIAFRNLC 1330 1340 1350 1360 1370 1380 HEYSYNGKII KVSATPPGRE CDLTTQYPVE LLIEEQLSLR DFVDAQGTDA HADVVKKGDN 1390 1400 1410 1420 1430 1440 ILVYVASYNE VDQLSKMLNE RGFLVTKVDG RTMKLGGVEI ITKGSSIKKH FIVATNIIEN 1450 1460 1470 1480 1490 1500 GVTLDVDVVV DFGLKVVPNL DSDNRLVSYC KIPISLGERI QRFGRVGRNK PGVALRIGET 1510 1520 1530 1540 1550 1560 IKGLVEIPSM IATEAAFLCF VYGLPVTTQN VSTSILSQVS VRQARVMCQF ELPIFYTAHL 1570 1580 1590 1600 1610 1620 VRYDGAMHPA IHNALKRFKL RDSEINLNTL AIPTSSSKTW YTGKCYKQLV GRLDIPDEIK 1630 1640 1650 1660 1670 1680 IPFYTKEVPE KVPEQIWDVM VKFSSDAGFG RMTSAAACKV AYTLQTDIHS IQRTVQIIDR 1690 1700 1710 1720 1730 1740 LLENEMKKRN HFNLVVNQSC SSHFMSLSSI MASLRAHYAK NHTGQNIEIL QKAKAQLLEF 1750 1760 1770 1780 1790 1800 SNLAIDPSTT EALRDFGYLE AVRFQSESEM ARGLKLSGHW KWSLISRDLI VVSGVGIGLG 1810 1820 1830 1840 1850 1860 CMLWQFFKEK MHEPVKFQGK SRRRLQFRKA RDDKMGYIMH GEGDTIEHFF GAAYTKKGKS 1870 1880 1890 1900 1910 1920 KGKTHGAGTK AHKFVNMYGV SPDEYSYVRY LDPVTGATLD ESPMTDLNIV QEHFGEIRRE 1930 1940 1950 1960 1970 1980 AILADAMSPQ QRNKGIQAYF VRNSTMPILK VDLTPHIPLK VCESNNIAGF PEREGELRRT 1990 2000 2010 2020 2030 2040 GPTETLPFDA LPPEKQEVAF ESKALLKGVR DFNPISACVW LLENSSDGHS ERLFGIGFGP 2050 2060 2070 2080 2090 2100 YIIANQHLFR RNNGELTIKT MHGEFKVKNS TQLQMKPVEG RDIIVIKMAK DFPPFPQKLK 2110 2120 2130 2140 2150 2160 FRQPTIKDRV CMVSTNFQQK SVSSLVSESS HIVHKEDTSF WQHWITTKDG QCGSPLVSII 2170 2180 2190 2200 2210 2220 DGNILGIHSL THTTNGSNYF VEFPEKFVAT YLDAADGWCK NWKFNADKIS WGSFTLVEDA 2230 2240 2250 2260 2270 2280 PEDDFMAKKT VAAIMDDLVR TQGEKRKWML EAAHTNIQPV AHLQSQLVTK HIVKGRCKMF 2290 2300 2310 2320 2330 2340 ALYLQENADA RDFFKSFMGA YGPSHLNKEA YIKDIMKYSK QIVVGSVDCD TFESSLKVLS 2350 2360 2370 2380 2390 2400 RKMKEWGFEN LEYVTDEQTI KNALNMDAAV GALYSGKKKQ YFEDLSDDAV ANLVQKSCLR 2410 2420 2430 2440 2450 2460 LFKNKLGVWN GSLKAELRPF EKLIENKTRT FTAAPIETLL GGKVCVDDFN NHFYSKHIQC 2470 2480 2490 2500 2510 2520 PWSVGMTKFY GGWNELLGKL PDGWVYCDAD GSQFDSSLSP YLINAVLRLR LSSMEEWDVG 2530 2540 2550 2560 2570 2580 QKMLQNLYTE IVYTPISTPD GTIVKKFKGN NSGQPSTVVD NTLMVVLAMY YALSKLGVDI 2590 2600 2610 2620 2630 2640 NSQEDVCKFF ANGDDLIIAI SPELEHVLDG FQQHFSDLGL NYDFSSRTRD KKELWFMSHR 2650 2660 2670 2680 2690 2700 ALSKDGILIP KLEPERIVSI LEWDRSAEPH HRLEAICASM IEAWGYTDLL QNIRRFYKWT 2710 2720 2730 2740 2750 2760 IEQEPYRSLA EQGLAPYLSE VALRRLYTSQ IATDNELTDY YKEILANNEF LRETVRFQSD 2770 2780 2790 2800 2810 2820 TVDAGKDKAR DQKLADKPTL AIDRTKDKDV NTGTSGTFSI PRLKKAAMNM KLPKVGGSSV 2830 2840 2850 2860 2870 2880 VNLDHLLTYK PAQEFVVNTR ATHSQFKAWH TNVMAELELN EEQMKIVLNG FMIWCIENGT 2890 2900 2910 2920 2930 2940 SPNISGVWTM MDGDEQVEYP IEPMVKHANP SLRQIMKHFS NLAEAYIRMR NSEQVYIPRY 2950 2960 2970 2980 2990 3000 GLQRGLVDRN LAPFAFDFFE VNGATPVRAR EAHAQMKAAA LRNSQQRMFC LDGSVSGQEE 3010 3020 NTERHTVDDV NAQMHHLLGV KGV
	Isoform P3N-PIPO polyprotein [UniParc]. See P0CK10.		–	–

References

[1]	"The nucleotide sequence of tobacco vein mottling virus RNA." Domier L.L., Franklin K.M., Shahabuddin M., Hellmann G.M., Overmeyer J.H., Hiremath S.T., Siaw M.F.E., Lomonossoff G.P., Shaw J.G., Rhoads R.E. Nucleic Acids Res. 14:5417-5430(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	Shaw J.G. Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	"A tyrosine residue in the small nuclear inclusion protein of tobacco vein mottling virus links the VPg to the viral RNA." Murphy J.F., Rychlik W., Rhoads R.E., Hunt A.G., Shaw J.G. J. Virol. 65:511-513(1991) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1874-1888, COVALENT RNA-LINKAGE OF VPG, URIDYLYLATION AT TYR-1878.
[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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X04083 Genomic RNA. Translation: CAA27720.1.
PIR	GNVSTV. A23647.
RefSeq	NP_056867.1. NC_001768.1.
3D structure databases
ProteinModelPortal	P09814.
SMR	P09814. Positions 2010-2221.
ModBase	Search...
Protein family/group databases
MEROPS	C04.003.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1494056.
Family and domain databases
InterPro	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. IPR014014. RNA_helicase_DEAD_Q_motif. 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. SSF52540. SSF52540. 2 hits.
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS51436. POTYVIRUS_NIA_PRO. 1 hit. PS51195. Q_MOTIF. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...
Other
PMAP-CutDB	P09814.

Entry information

Entry name

POLG_TVMV

Accession

Primary (citable) accession number: P09814
Secondary accession number(s): Q84898 , Q84899, Q84900, Q84901, Q84902

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	May 30, 2000
Last modified:	May 29, 2013
This is version 121 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program