A4KZ49 (POLG_TRMVU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 10 chains: P1 proteinase Alternative name(s): N-terminal protein EC=3.4.-.- 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	Triticum mosaic virus (isolate Triticum aestivum/United States/U06-123/2006) (TriMV) [Complete proteome]
Taxonomic identifier	1289472 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Poacevirus › Triticum mosaic virus
Virus host	Avena sativa (Oat) [TaxID: 4498] Hordeum vulgare (Barley) [TaxID: 4513] Secale cereale (Rye) [TaxID: 4550] Triticum aestivum (Wheat) [TaxID: 4565] x Triticosecale [TaxID: 49317]

Protein attributes

Sequence length	3112 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	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 By similarity. Nuclear inclusion protein B: a RNA-dependent RNA polymerase that plays an essential role in the virus replication By similarity. 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 By similarity.
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 By similarity.
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 RdRp catalytic domain.

Ontologies

Keywords
Biological process	Viral 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 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...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 3112	3112	Genome polyprotein		PRO_0000420027
	Chain	1 – 383	383	P1 proteinase Potential		PRO_0000395486
	Chain	384 – 850	467	Helper component proteinase Potential		PRO_0000395487
	Chain	851 – 1148	298	Protein P3 By similarity		PRO_0000395488
	Chain	1149 – 1204	56	6 kDa protein 1 By similarity		PRO_0000395489
	Chain	1205 – 1852	648	Cytoplasmic inclusion protein By similarity		PRO_0000395490
	Chain	1853 – 1902	50	6 kDa protein 2 By similarity		PRO_0000395491
	Chain	1903 – 2095	193	Viral genome-linked protein By similarity		PRO_0000395492
	Chain	2096 – 2328	233	Nuclear inclusion protein A By similarity		PRO_0000395493
	Chain	2329 – 2818	490	Nuclear inclusion protein B By similarity		PRO_0000395494
	Chain	2819 – 3112	294	Capsid protein By similarity		PRO_0000288836
Regions
	Domain	1278 – 1429	152	Helicase ATP-binding
	Domain	1444 – 1627	184	Helicase C-terminal
	Domain	2096 – 2311	216	Peptidase C4
	Domain	2569 – 2687	119	RdRp catalytic
	Nucleotide binding	1291 – 1298	8	ATP By similarity
	Motif	1379 – 1382	4	DECH box
Sites
	Active site	737	1	For helper component proteinase activity By similarity
	Active site	809	1	For helper component proteinase activity By similarity
	Active site	2140	1	For nuclear inclusion protein A activity By similarity
	Active site	2174	1	For nuclear inclusion protein A activity By similarity
	Active site	2243	1	For nuclear inclusion protein A activity By similarity
	Site	383 – 384	2	Cleavage; by P1 proteinase Potential
	Site	850 – 851	2	Cleavage; by HC-pro Potential
	Site	1148 – 1149	2	Cleavage; by NIa-pro By similarity
	Site	1204 – 1205	2	Cleavage; by NIa-pro By similarity
	Site	1852 – 1853	2	Cleavage; by NIa-pro By similarity
	Site	1902 – 1903	2	Cleavage; by NIa-pro By similarity
	Site	2095 – 2096	2	Cleavage; by NIa-pro By similarity
	Site	2328 – 2329	2	Cleavage; by NIa-pro By similarity
	Site	2818 – 2819	2	Cleavage; by NIa-pro By similarity
Experimental info
	Sequence conflict	2819	1	S → E AA sequence Ref.2

Sequences

	Sequence		Length	Mass (Da)
	A4KZ49 [UniParc]. Last modified July 13, 2010. Version 3. Checksum: 5B066BBD6C5D5151	FASTA	3,112	352,841
	10 20 30 40 50 60 MSSKKMMWVP KSAHKAPVVS REPVIRKKEW VARQIPKYIP VSNPSDCRDE ISQTLLHFDS 70 80 90 100 110 120 EEAVYDFVWR FPMGSIFWDT NGRIKPVVNC LLRATRMNLD YDVAADVYVC RDCLSCASSY 130 140 150 160 170 180 MYFSNYHYDC RELRENHEAV VSCKYEQHIV STFDVFPRYC TQEIEQNVVN WMTETLERYD 190 200 210 220 230 240 NEPLRIEKQL QFYNHKTEQM ESRVQEVQVT TAEYAVSDTY VPQQLSRKGS VSAKLTQRRA 250 260 270 280 290 300 NKIIMRTHEV ENLIRETIDL CDERQIPITF VDVKHKRCLP RIPLRHMQAK PDISEIVEQG 310 320 330 340 350 360 DMYNEVGQFI EQYQNLAEPF RVIRDYEVTR GWSGVILHRD DLALDPQTQA RCLNNLFVVM 370 380 390 400 410 420 GRCEHGHLQN ALRPDCLEGL TYYSDTFGKV FNESLVKHHP GKHQFRIGSR TDYEWEELAM 430 440 450 460 470 480 WVNAVCPVSF RCADCRPPQS LNEYIENIRM SKAMAELAGR QDALSKTLHK WTTMLISSVL 490 500 510 520 530 540 TTEIRARDNL EPIQERIFTR NMPLGPLYDV AGAMNRAVID IQTAVQNMQL SIGNSNMNEQ 550 560 570 580 590 600 QRNQTLLNEI NKIKQHSFMQ TKEMLSRFEN IAQTYQNIIS SASQPLSIHS MRQLMMDSRM 610 620 630 640 650 660 DESFEFDIMR KKGSIASIAP MAFRTFEDIY SQPGVYNQKW LNLTPSGRFQ TDIDYLRLDL 670 680 690 700 710 720 PIDVIQKKKH VVNRNEIKEE TCYVIVGQVN VSFCEVVARC FVPIPHVLRV GSPQNPTMIK 730 740 750 760 770 780 IQDQEGGKTL VPKSGFCYVL QLVLMLGYVP DQLTAAFVKD VGIVVESLGP WPLFVDYLGA 790 800 810 820 830 840 IKNLIIRYPT TIKAPTALHI VDHVDTVIHV MTTLGCVNKG EHYLTLQSVA QLHDAAMTVN 850 860 870 880 890 900 IETFKDYRIG GVVPQLKHML QSEEHMLEVL EAKPQWLVHL LLSPTQIWAL SQSVVKYQVI 910 920 930 940 950 960 HKVMTSNPDL AVALAQLVAI SSNFSIFKNT EHVIQKYFEV SKQLQNVSGV ILGEHNEYFE 970 980 990 1000 1010 1020 TAFAQYSALR FSTDVVLLMD QFSTRKKTLD DLEDYYRKTI PSILIECGLL GPSDFGWRKR 1030 1040 1050 1060 1070 1080 LVRGVVDRGS GLKSTVKSLG SFSTKEKWIS WSGLGSGTIT CVKFPFVCLQ RSGSWLYSST 1090 1100 1110 1120 1130 1140 KTTAFNAVWM AGIKCVKSNV RSILLDSALY GAITLALLCA IKLIRKAFRF VEGLIKEDTS 1150 1160 1170 1180 1190 1200 DDEDYVLHAK AASDSLYIQC LAWLALVVGC FNSGLANDIY FSTTKYRTLL DMVKTAHSDS 1210 1220 1230 1240 1250 1260 FVFHAGDEEE GEIVELITRD NFVDYVYNHS DPLMEFDSET LLGWYTRISY QGRVLEHPLR 1270 1280 1290 1300 1310 1320 VGTNCHLTRE NVDEIAKNIA TGAGNEFIVV GDVGSGKSTK LPIAVSTYGP VLILVPSREL 1330 1340 1350 1360 1370 1380 VNNLCSSIWH VGKKQASTYM MNCITRGTSN ISIMTYGYAL ALFSHCPIEL QKYRFIQMDE 1390 1400 1410 1420 1430 1440 CHEFSSHMIT FYSWWRESGK FTKLFKTTAT PPGTVIKGGC VPTNHKVDVI EIRDVSVEEF 1450 1460 1470 1480 1490 1500 CRRSIDSHAE GLRSLMPNGG RVIMFVPSRR ECELARSSLI SIPGARTWVV YRAAATQATK 1510 1520 1530 1540 1550 1560 LVAELADDKH YFQIIITTTV LQNGVNLDPD CVVDFGQTFE AAYDRDSRQL GVRRRNINPG 1570 1580 1590 1600 1610 1620 ELIQRVGRVG RNKPGKFIQV GKRLEHEVVP NSCCVTDAIL MSFTLELAPF ISSHLIDEVN 1630 1640 1650 1660 1670 1680 FVTREQVRTA MKFSAPLLFM IHYVRRDGRM LNGYYQQLKG LLLQTSDVAL CDTLVGDAET 1690 1700 1710 1720 1730 1740 NSFLTLRQYQ LRGIIEAQEV LPDLPIPFYS SEFALPFYLE IGQITKEAIR ARSFTLRIKT 1750 1760 1770 1780 1790 1800 PDVKKAVMRL STSATQIDQT IGILRTRLQL TRERLSKFSE LKATAHNLRL TPIFNTCFDM 1810 1820 1830 1840 1850 1860 GAAKSESTLR ASLTAGEELL SALELARTEK SDKALEKLIL DNPVLGDCLV FHGGPEEYFD 1870 1880 1890 1900 1910 1920 QTLFQTSTGL INKYTVGIAC LTVGLGCTIW YYLKKREKYV MHGKVHTRET GLTTNHLFVP 1930 1940 1950 1960 1970 1980 GMKEHIQEWT GGDHEIGNRF GEAYKRRFIG RQPTEEQKLS KEKWDKREGQ QTSVYKTLYD 1990 2000 2010 2020 2030 2040 LDPTKFKYVV VECPDFDLKK KLNRQEKKQL DTTIVEACRT RMLDKGQHDF KDVERATVYL 2050 2060 2070 2080 2090 2100 FNDNGVGHKV QLTPHNPLAV SRTTTHPVGF PAEAGRLRQT GQAMEMTPEE LEKALDDNYV 2110 2120 2130 2140 2150 2160 PHSRCQIDIS HLHRHLAIVN TGGMSTQCFI TQTMCVAPYH LAMGFKDNTK LTIYCSNGVY 2170 2180 2190 2200 2210 2220 VMPVPKVEKM ENMDLVVFRM PQDFPPLKRC ATIREPKSSD EVTLITGKRT THGIQLQFSK 2230 2240 2250 2260 2270 2280 VVSIDRKSDT VWKYMIDSVP GVCGGMVMCV EDGCVVGFHS AAAIRNKVSN GSIFTPVTPQ 2290 2300 2310 2320 2330 2340 LLDSLQSSEG HLFDWYFNDD LISWKGVPTN MDPRNFPVSE TISEFIFHND SKGHGTDKYY 2350 2360 2370 2380 2390 2400 GENLTIEGRV LQSFNTRHVV KGLDDAFAEY VNKFGEPPAD TFTHLPSDLS SDAFYKDFMK 2410 2420 2430 2440 2450 2460 YSTPVEVGTV NIENFEKAVQ AVVELLEQQG FEQGEFSPEM DFYKILNSFN LDTAMGALYQ 2470 2480 2490 2500 2510 2520 CKKKDVLPMA SHEQLATWFW NSLENLATGK LGLWKASLKA ELRPKEKVLE KKTRVFTAAP 2530 2540 2550 2560 2570 2580 FDVSFGAKAF VDDFNNKFYA TQAGSNWTVG INKFNCGWDE LARRFNPDWK FIDADGSRYD 2590 2600 2610 2620 2630 2640 SSLTPLLFNA VLRIRQHFLR ANGFERRMLS NFYTQLVWTP ISTITGQIVK KNKGGPSGQP 2650 2660 2670 2680 2690 2700 STVVDNTMML MIAVEYAKLQ YGVTDLKYVC NGDDLILNAP QGVCETIRAN FSHSFKELGL 2710 2720 2730 2740 2750 2760 TYEFEQEVDS IDQVEYMSHK WIDCGGVLIP KLKPERIVSV LQWNKSLDLA SQANKINAAW 2770 2780 2790 2800 2810 2820 IESFGYGDLS KFIREYANWW GERNGQVGFL CSEEKVASLY LTNDVTIHTE EHDEFVFHSG 2830 2840 2850 2860 2870 2880 ADQSGVVKDQ TGDKAEGSGT KTEDPPNQTT DPVNNPSNGG NKDAPQNLNA TVVTKSYTYI 2890 2900 2910 2920 2930 2940 PPIMKSLVTI DTAKKMADYT PPDALISTQA CTLEQFGRWA NAAANGLGLS MQAFQTDVVP 2950 2960 2970 2980 2990 3000 YWIYWCIVNS ASDEHKKLSS WTKVNMTIDD ATGQINLNEG EAQTIYEMSP MFDEAKPTLR 3010 3020 3030 3040 3050 3060 AVMRHFGALA YRWVKFSIAK RKPIIPHNAI KAGLMDVTYF PCCIDFVTVD QLSPQEQNVR 3070 3080 3090 3100 3110 NQVINARVSD TPRALFKHAQ RAGAGEEDTN LRRDDDANYG RTRVGGAMFG TR

References

[1]	"The complete genome sequence of Triticum mosaic virus, a new wheat-infecting virus of the High Plains." Fellers J.P., Seifers D., Ryba-White M., Martin T.J. Arch. Virol. 154:1511-1515(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Triticum mosaic virus: A new virus isolated from wheat in Kansas." Seifers D.L., Martin T.J., Harvey T.L., Fellers J.P., Stack J.P., Ryba-White M., Haber S., Krokhin O.V., Spicer V., Lovat N., Yamchuk A., Standing K.G. Plant Dis. 92:808-817(2008) Cited for: PROTEIN SEQUENCE OF 2819-2918; 2953-2968; 2988-3000; 3005-3012 AND 3016-3112.

Cross-references

Sequence databases
EMBL GenBank DDBJ	FJ263671 Genomic RNA. Translation: ABO41208.2.
RefSeq	YP_002956073.1. NC_012799.1.
3D structure databases
ProteinModelPortal	A4KZ49.
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. IPR025910. P1_Ser_Pept_dom. 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. PF13611. Peptidase_S76. 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. [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_TRMVU

Accession

Primary (citable) accession number: A4KZ49

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 29, 2007
Last sequence update:	July 13, 2010
Last modified:	May 1, 2013
This is version 35 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program