P17765 (POLG_BYMV) 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	Bean yellow mosaic virus [Complete proteome]
Taxonomic identifier	12197 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Papaver somniferum (Opium poppy) [TaxID: 3469] Arachis hypogaea (Peanut) [TaxID: 3818] Crotalaria [TaxID: 3828] Glycine max (Soybean) (Glycine hispida) [TaxID: 3847] Lupinus luteus (European yellow lupin) [TaxID: 3873] Medicago sativa (Alfalfa) [TaxID: 3879] Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885] Pisum sativum (Garden pea) [TaxID: 3888] Trifolium repens (Creeping white clover) [TaxID: 3899] Trifolium subterraneum (Subterranean clover) [TaxID: 3900] Vicia faba (Broad bean) (Faba vulgaris) [TaxID: 3906] Vicia sativa (Spring vetch) (Tare) [TaxID: 3908] Canna [TaxID: 4627] Robinia pseudoacacia (Black locust) [TaxID: 35938] Gladiolus [TaxID: 49747] Eustoma [TaxID: 52517] Trifolium pratense (Red clover) [TaxID: 57577] Freesia [TaxID: 58987] Trifolium incarnatum (Crimson clover) [TaxID: 60916] Trifolium hybridum (Alsike clover) [TaxID: 74517] Trigonella foenum-graecum (Fenugreek) [TaxID: 78534] Trifolium vesiculosum [TaxID: 97047]

Protein attributes

Sequence length	3056 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 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. 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_0000040256
	Chain	285 – 741	457	Helper component proteinase Potential		PRO_0000040257
	Chain	742 – 1089	348	Protein P3 Potential		PRO_0000040258
	Chain	1090 – 1142	53	6 kDa protein 1 By similarity		PRO_0000040259
	Chain	1143 – 1777	635	Cytoplasmic inclusion protein By similarity		PRO_0000040260
	Chain	1778 – 1830	53	6 kDa protein 2 By similarity		PRO_0000040261
	Chain	1831 – 2021	191	Viral genome-linked protein By similarity		PRO_0000040262
	Chain	2022 – 2264	243	Nuclear inclusion protein A By similarity		PRO_0000040263
	Chain	2265 – 2783	519	Nuclear inclusion protein B By similarity		PRO_0000040264
	Chain	2784 – 3056	273	Capsid protein By similarity		PRO_0000040265
Regions
	Domain	1214 – 1366	153	Helicase ATP-binding
	Domain	1385 – 1544	160	Helicase C-terminal
	Domain	2022 – 2240	219	Peptidase C4
	Domain	2507 – 2630	124	RdRp catalytic
	Nucleotide binding	1227 – 1234	8	ATP Potential
	Motif	335 – 338	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	593 – 595	3	Involved in virions binding and aphid transmission By similarity
	Motif	1316 – 1319	4	DECH box
	Motif	1871 – 1878	8	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	627	1	For helper component proteinase activity By similarity
	Active site	700	1	For helper component proteinase activity By similarity
	Active site	2067	1	For nuclear inclusion protein A activity By similarity
	Active site	2102	1	For nuclear inclusion protein A activity By similarity
	Active site	2172	1	For nuclear inclusion protein A activity By similarity
	Site	294 – 295	2	Cleavage; by P1 proteinase Potential
	Site	711 – 712	2	Cleavage; by HC-pro Potential
	Site	1100 – 1101	2	Cleavage; by NIa-pro By similarity
	Site	1152 – 1153	2	Cleavage; by NIa-pro By similarity
	Site	1787 – 1788	2	Cleavage; by NIa-pro By similarity
	Site	1840 – 1841	2	Cleavage; by NIa-pro By similarity
	Site	2021 – 2022	2	Cleavage; by NIa-pro By similarity
	Site	2274 – 2275	2	Cleavage; by NIa-pro By similarity
	Site	2793 – 2794	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1893	1	O-(5'-phospho-RNA)-tyrosine By similarity
Natural variations
	Natural variant	2775	1	D → G.
	Natural variant	2805	1	D → N.
	Natural variant	2855	1	L → F.
	Natural variant	2862	1	E → K.
	Natural variant	2897	1	Q → R.
	Natural variant	2975	1	G → E.
	Natural variant	2994	1	K → E.
	Natural variant	3017	1	G → A.

Sequences

	Sequence		Length	Mass (Da)
	P17765 [UniParc]. Last modified June 21, 2005. Version 2. Checksum: BA4D2F2D2D4624B3	FASTA	3,056	347,722
	10 20 30 40 50 60 MTTINIGTIP VVINQNADTQ MGEGTKNIFP IVKDFVDPFA DLEMRCAERV KRMGELCFSK 70 80 90 100 110 120 KGRYITMIPK PDYIKAREKE QREEELNFQN SEHVLNSLDT TCTPEHHSSR NNGMQVSFKT 130 140 150 160 170 180 QHYKRTFRKP RIQAKKRDLK GQHTIHYVAK ELLSIVKKRD MVLEVVDKRK HANFATFRRY 190 200 210 220 230 240 GKTYGMHITL NHMVRKRRRV DVTLNKLMTE IAMHCAIPFE CLNTLTLRKG HSGLVLQTET 250 260 270 280 290 300 VPNVHKIKSK ITIVRGVVNE GNIPVLIDAR KKLSGRDMST IREFSAGDLF WKGYNQTFID 310 320 330 340 350 360 NRPTDLNHQC TSDLNVTQCG SVMALLTLAL FPCGRITCKK CVENFLNQNN KERFNNASVF 370 380 390 400 410 420 INQVIQLLEK GFSEFKHSKE ILLMFKERLQ MENPATDQCM EIAKATAALP EAPFSHIKEI 430 440 450 460 470 480 NNVLLKYGSL SNEEVGGASK HLLEVVRYIR NRTDSIQRND LSKFRNKISS KTHINLDLMC 490 500 510 520 530 540 DNQLDKNANF VWGQRAYHAK RFLSNYFNEI NPSEGYDKFI FRKLPNGARE LAIGRLIMPT 550 560 570 580 590 600 NFEAFREQMK GKMIDNGPIG KDCVSRMRGS FCYPCCCTTD DVGTAVISDF KMPTKYHLVL 610 620 630 640 650 660 GGNDLAKYIK LPTDTTGNMY IAKDGFCHIN IFFAMLVNVS EEKSKDFTKM VRDQIMPKLG 670 680 690 700 710 720 EWPTMMDVAT ACWQLTVWFP DTLSAELPRI LVDHKLGIMH VLDSYGSISA GYHVLKANIV 730 740 750 760 770 780 SQLIKFASDD LESELKYYRV GGDCNFGSRV RIDTKFLLKS IYRPDLLERI IEHEPFVLVL 790 800 810 820 830 840 AMQSPAVLLA LFNSASLEKA VQYWMHREMQ VSHIMTLLAV LASNVSASKL LTTQFEIIEA 850 860 870 880 890 900 SAPQILAEMD KVHLPMHSIH SANVFLMNMS ESRETDKTID ELGFYSFKKS SRILMEKTLM 910 920 930 940 950 960 ADLEEQWQGL GLLERLSLIK RSWRVRAKYS SFAIQREEPG IRDKFTTSLK LSGAQIKQQL 970 980 990 1000 1010 1020 LAQKDQAVHF VERRIEGTKK FVANQSISLI KMCLPRLADI VNILTVIALL NAILAFMLDH 1030 1040 1050 1060 1070 1080 IKRFNEARRI AQEKKEKQHL KELNTLYNKY WDNEKPTYLE FKSDVIEKLP HTLATFEKYY 1090 1100 1110 1120 1130 1140 FEDDKYTFQA KPNDMVALEK IIAVTALVLM IFDAERSDCV YKVLNKLKGI LSTTTQDAYR 1150 1160 1170 1180 1190 1200 FQSLDTSKTL LEEKEMTIDF EINEGEVKAF SGTQTTFSEW WDNQLQNGNV ITHYRTEGQF 1210 1220 1230 1240 1250 1260 MEFTRANAQP VANEIAHNDA HDILVRGAVG SGKSTGLPFY LSNKGKVLMI ESTRPLAENV 1270 1280 1290 1300 1310 1320 FKQLKSEPFY ASPTLRMRGT TSYGASPITI MTSGYALHYY ANNPAMMKEY KFVIIDECHV 1330 1340 1350 1360 1370 1380 HDANAIAFVS LLKEYSFDGK LIKVSATPPG REVEFTTQYP VTLVTEESLS FEQFVSQQGT 1390 1400 1410 1420 1430 1440 GANCDMLDVC DNILVYVASY NEVDQLSKML LDRGHIVTKV DGRTMKNGKT EIESKGSRSK 1450 1460 1470 1480 1490 1500 RHFIVATNII ENGVTLDIEG VVDFGLKVVP ELDVDNRLMR YTKQNVSYGE RIQRLGRVGR 1510 1520 1530 1540 1550 1560 HKAGKALRIG VTEKGLVKPP SVITTEAAFY CFAYGLPVMA EGVTPSLLSK CTVQQARSMM 1570 1580 1590 1600 1610 1620 SFELPIMYTV NLVRFDGTMH PSVHNLLKPY KLRDSNVVLN KMAIPHGNVR NWPTVRDFKC 1630 1640 1650 1660 1670 1680 MGVRIDAPED TRVPFHARDI PDKLHKEIFE VCCKYKGDAG FSKLNVVNAC KIAYTLQTDP 1690 1700 1710 1720 1730 1740 SSIQRTIKIL DELIAREQQK REYFQNVANT SCAGSSYSLS NIINAIRARS TSDYTQENLS 1750 1760 1770 1780 1790 1800 VLHSARAQLL EFKNINSDFS NLSTLSEFGA LECLQFESLQ EISKHLQLKG HWNKPVLIQD 1810 1820 1830 1840 1850 1860 FLIAAGVLGG GCWMLYQYFK QETSKAFVFQ GKNRRTKQKL RFRDARDMKG RMEVYADEGT 1870 1880 1890 1900 1910 1920 IVENFGSKYT KKGKVRGTTT GMGTKTRRFT NMYGFDPTEY SFARYLDPIT GETLDEQPIT 1930 1940 1950 1960 1970 1980 NLNLVSEHFQ EMRRKYRENE IMESQQFAAN PRIEAYFVKD AGQKVLKVDL TPHKPLLYSD 1990 2000 2010 2020 2030 2040 KFGNIMGYPE REGELRQTGA AEFIDPKELP EPKESTDFDF ESLSKIGGLR DYNPIAANVC 2050 2060 2070 2080 2090 2100 LLENESAEYC DEIYGIGYGN VIITNQHLFR HNNGELTIKS KHGTFKCKNT CALKLLPIEG 2110 2120 2130 2140 2150 2160 HDLLLIQMPK DFPVFPQKLR FREPTHEDKI VLVSTNFQEK SFSSVVSESS NISRVKQANF 2170 2180 2190 2200 2210 2220 FKHWISTVAG QCGNPMVSTK DGFIVGIHSL TAVSGDLNVF TSIPPNFEDE VLKQMSKKSW 2230 2240 2250 2260 2270 2280 CCGWKLNMSQ IGWDGIKIVD DQPKDPFPVS KMVGLLNDLQ LSFQSAKNTK WLLERAHGNI 2290 2300 2310 2320 2330 2340 KAVAQASSAL VTKHVVKGKC RLFEVYLTTD EEAEKFFRPL MGAYQKSRLN KEAYVKDLMK 2350 2360 2370 2380 2390 2400 YATPIEVGLV DTRCFERSFE KVQNMLELKG FSKCNYVTYG PDILSALNMK AAMGALYSGK 2410 2420 2430 2440 2450 2460 KKDHFSEISE EKFDNILQAS CERLYSGRMG VWNGSLKAEL RPQEKVLANK TRSFTAAPID 2470 2480 2490 2500 2510 2520 TLLAGKVCVD DFNNKFYSLH LKIPSTVGIT KFYGGWDRLL DSLPDGWVYC DADGSQFDSS 2530 2540 2550 2560 2570 2580 LTPYLLNAVL EMRLRLMEEW DLGEQMLKNL YTEIVYTPIL TPDGTIVKKF KGNNSGQPST 2590 2600 2610 2620 2630 2640 VVDNTLMVIM AVYYAAEKLG IKGNLEDTLV FFANGDDLLI AIKPECESYL DKFEGLFSEL 2650 2660 2670 2680 2690 2700 GLKYDFSSRT KNKGDLWFMS HRGIQIDGMW IPKLEEERIV SILEWDRAIQ PEHRLEAICA 2710 2720 2730 2740 2750 2760 AMIEAWGYPT LLNHIRKFYL WVLGQAPYSQ LSAEGKAPYI SEVALKHLYT EEKVTPTELE 2770 2780 2790 2800 2810 2820 RYNIALIDCF ESESDEVLTC RFQSDQEQLN AGEEKKDKRK KNEGDPNKDS EGQSVRQIVP 2830 2840 2850 2860 2870 2880 DRDVNAGTVG TFSVPRLKKI AGKLNIPKIG GKIVLNLDHL LEYNPPQDDI SNVIATQAQF 2890 2900 2910 2920 2930 2940 EAWYNGVKQA YEVEDSQMGI ILNGLMVWCI ENGTSGDLQG EWTMMDGEEQ VTYPLKPILD 2950 2960 2970 2980 2990 3000 NAKPTFRQIM SHFSEVAEAY IEKRNATERY MPRYGLQRNL TDYGLARYAF DFYKLTSRTP 3010 3020 3030 3040 3050 VRAREAHMQM KAAAVRGKST RLFGLDGNVG TDEENTERHT AGDVNRDMHT MLGVRI

References

[1]	"The complete nucleotide sequence of isolate BYMV-GDD of Bean yellow mosaic virus, and comparison to other potyviruses." Hammond J., Hammond R.W. Arch. Virol. 148:2461-2470(2003) [PubMed: 14648299] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate GDD.
[2]	"Molecular cloning, sequencing and expression in Escherichia coli of the bean yellow mosaic virus Capsid protein gene." Hammond J., Hammond R.W. J. Gen. Virol. 70:1961-1974(1989) [PubMed: 2671258] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2775-3056.
[3]	"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	AY192568 Genomic RNA. Translation: AAP30002.1. D00490 Genomic RNA. Translation: BAA00378.1.
PIR	JU0115.
3D structure databases
ProteinModelPortal	P17765.
SMR	P17765. Positions 2030-2243.
ModBase	Search...
Protein family/group databases
MEROPS	S30.002.
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_BYMV

Accession

Primary (citable) accession number: P17765
Secondary accession number(s): Q65887, Q6Y1D8

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	June 21, 2005
Last modified:	November 16, 2011
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program