Q89330 (POLG_ZYMVR) 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	Zucchini yellow mosaic virus (strain Reunion Island) (ZYMV) [Complete proteome]
Taxonomic identifier	117129 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Citrullus lanatus (Watermelon) (Citrullus vulgaris) [TaxID: 3654] Cucumis melo (Muskmelon) [TaxID: 3656] Cucumis sativus (Cucumber) [TaxID: 3659] Cucurbita pepo (Vegetable marrow) (Summer squash) [TaxID: 3663]

Protein attributes

Sequence length	3083 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 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 – 314	314	P1 proteinase Potential		PRO_0000040510
	Chain	315 – 769	455	Helper component proteinase Potential		PRO_0000040511
	Chain	770 – 1115	346	Protein P3 By similarity		PRO_0000040512
	Chain	1116 – 1167	52	6 kDa protein 1 By similarity		PRO_0000040513
	Chain	1168 – 1801	634	Cytoplasmic inclusion protein By similarity		PRO_0000040514
	Chain	1802 – 1854	53	6 kDa protein 2 By similarity		PRO_0000040515
	Chain	1855 – 2044	190	Viral genome-linked protein By similarity		PRO_0000040516
	Chain	2045 – 2287	243	Nuclear inclusion protein A By similarity		PRO_0000040517
	Chain	2288 – 2804	517	Nuclear inclusion protein B By similarity		PRO_0000040518
	Chain	2805 – 3083	279	Capsid protein By similarity		PRO_0000040519
Regions
	Domain	1239 – 1391	153	Helicase ATP-binding
	Domain	1410 – 1569	160	Helicase C-terminal
	Domain	2045 – 2263	219	Peptidase C4
	Domain	2529 – 2653	125	RdRp catalytic
	Nucleotide binding	1252 – 1259	8	ATP Potential
	Motif	365 – 368	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	621 – 623	3	Involved in virions binding and aphid transmission By similarity
	Motif	1341 – 1344	4	DECH box
	Motif	1894 – 1903	10	Nuclear localization signal Potential
Sites
	Active site	267	1	For P1 proteinase activity By similarity
	Active site	655	1	For helper component proteinase activity By similarity
	Active site	728	1	For helper component proteinase activity By similarity
	Active site	2090	1	For nuclear inclusion protein A activity By similarity
	Active site	2125	1	For nuclear inclusion protein A activity By similarity
	Active site	2195	1	For nuclear inclusion protein A activity By similarity
	Site	314 – 315	2	Cleavage; by P1 proteinase Potential
	Site	769 – 770	2	Cleavage; by HC-pro Potential
	Site	1115 – 1116	2	Cleavage; by NIa-pro By similarity
	Site	1167 – 1168	2	Cleavage; by NIa-pro By similarity
	Site	1801 – 1802	2	Cleavage; by NIa-pro By similarity
	Site	2044 – 2045	2	Cleavage; by NIa-pro By similarity
	Site	2287 – 2288	2	Cleavage; by NIa-pro By similarity
	Site	2804 – 2805	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1918	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q89330 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 55E51B455C20C537	FASTA	3,083	351,161
	10 20 30 40 50 60 MAAIMIGSIS VPIVESARCA TVQTGNRVNI VAPGHVAVCK PQMKSHSYYK HASEKLSKQA 70 80 90 100 110 120 SESINILNSF FDTDPEMRFR LTRNEMSKVK KGPNGRMILR KPRAQRVLER ISFEKIEKGA 130 140 150 160 170 180 ERQVLPWRVY ATVTSIINTF TDERNGIANS SLRSPFYKRS CRKEKKKIVC ENVVRSASVN 190 200 210 220 230 240 NLCDRVLKIA REKNIPVEMI GKKKNRHTLT FKNFKGSFIG KVSLAHERGQ MRHVEMSYEQ 250 260 270 280 290 300 FGFILQAICR VTNTRCVRDE DIKPGCSGWV LGDDHELTQK FSRLPCLVIR GRDDEGIVNA 310 320 330 340 350 360 LEPVFFYDDV DHYSSQPEVQ FFQGWRRMFD NFKPSSDHVC KVDHGNEECG ELAAIFSQAL 370 380 390 400 410 420 FPVVKLSCQT CREKLSRVSF EEFKDSLAIN FTVHKSEWDS LKENPHHDNV LKLIKGATQA 430 440 450 460 470 480 TQNLKLSSEV MKLVQNHTST HMKQIQDINR ALMKGSLVTQ DELDLALKQL LEMTQWFKNH 490 500 510 520 530 540 MHLTGEEALK TFRNKRSSKA MINPSLLCDN QLDKNGNFVW GERGYHSKRL FKNFFEEVIP 550 560 570 580 590 600 SEGYTKYIVR NFPNGTRKLA IGSLIVPLNL DRARTALLGE SIEKEPLTSA CVSQQNGNYI 610 620 630 640 650 660 HSCCCVTMDD GTPMYSDVKS PTKRHLVIGA SGDPKYIDLP ASEADRMYIA KEGYCYLNIF 670 680 690 700 710 720 LAMLVNVNEN EAKDFTKMIR DVLIPMLGQW PSLMDVATAA YILGVFHPET RCAELPRILV 730 740 750 760 770 780 DHATQTMHVI DSYGSLTVGY HVLKAGTVNH LIQFASNDLQ SEMKHYRVGG TPTQRIKLEE 790 800 810 820 830 840 QLIKGIFKPK LMMQLLQDDP YVLILGMVSP TILVHMYRMR HFERGIEMWI KRDHEVGKIF 850 860 870 880 890 900 VILEQLTRKV ALTEVLVDQL DLISEASPHL LEIMKGCQDN QRAYVPALDL LTVQVEREFS 910 920 930 940 950 960 NKELKVNGYP DLQQTLYDMR EKIYAKQLHD SWQELSLLEK SCVTVRLKRF SIFTERKLTQ 970 980 990 1000 1010 1020 QAKDGKRVSS LQFVHECFIT TRVHAKSIRD VGMRKFNEAL VGTCKFLFTC GFKIFARCYS 1030 1040 1050 1060 1070 1080 DIIYLVNVCL IFSLVLQMSN TVRSMISATR EEKERALANK ADENERTLMH MYHIFSKKQD 1090 1100 1110 1120 1130 1140 DAPLYSEFLE HVRNVRPDLE ETLLYMAGAE IVTPQAKSAV QVQFEKIIAV VALLTMCFDA 1150 1160 1170 1180 1190 1200 ERSDAIFKIL TKLKTVFGTV GETVRLQGLE DIENLEDDKK LTIDFDINTN EAQSSTTFDV 1210 1220 1230 1240 1250 1260 HFDDWWNRQL QQNRTVPHYR TTGKFLEFTR NTAAFVANEI ASSNEGEFLV RGAVGSGKST 1270 1280 1290 1300 1310 1320 SLPAHLAKKG KVLLLEPTRP LAENVSRQLA GDPFFQNVTL RMRGLSCFGS SNITVMTSGY 1330 1340 1350 1360 1370 1380 AFHYYVNNPH QMMEFDFIII DECHVTDSAT IAFNCALKEY NFAGKLIKVS ATPPGRECDF 1390 1400 1410 1420 1430 1440 DTQFAVKVKT EDHLSFQAFV GAQRTGSNAD MIQHGNNILV YVASYNEVDM LSKLLTERQF 1450 1460 1470 1480 1490 1500 SVTKVDGRTM QLGKTTIETH GTSQKPHFIV ATNIIENGVT LDVDCVVDFG LKVVAELDSE 1510 1520 1530 1540 1550 1560 SRCVRYSKKP VNYGERIQRL GRVGRSKPGT ALRIGHTEKG IENIPEFIAT EAAALSFAYG 1570 1580 1590 1600 1610 1620 LSVTTHGVST NILGKCTVKQ MKCALNFELT PFFTTHLIRH DGSMHPLIHE ELKQFKLRDS 1630 1640 1650 1660 1670 1680 EMVLNKVALP HQFVSQWMTQ GDYEHIGVHI QCNENTRIPF YTNGIPDRVY EKIWKCIQEN 1690 1700 1710 1720 1730 1740 KNDALFGRLS SACSTKVSYT LSTDPAALPR TIAIIDHLLA EEMMKRNHFD MISSAVTGYS 1750 1760 1770 1780 1790 1800 FSLAGIADSF RKRYMRDHTA HNIAILQQAR AQLLEFDSKN VNINNLSDLE GIGVIKSVVL 1810 1820 1830 1840 1850 1860 QSKQEVSNFL GLRGKWDGRK FANDVILAIM TLLGGGWFMW EYFTKKVNEP VRVESKKRRS 1870 1880 1890 1900 1910 1920 QKLKFRDAYD RKVGREIFGD DETIGRTFGE AYTKRGKVKG NNSTKGMGRK TRNFVHLYGV 1930 1940 1950 1960 1970 1980 EPENYSFIRF VDPLTGHTLD ESTHTDISLV QEEFGNIREK FLENDLISRQ SIINKPGIQA 1990 2000 2010 2020 2030 2040 YFMGKGTAEA LKFDFTPHVP SLSCSNSNAH AGYPERENEL RQTGTPVKVS LKDVPEKNEH 2050 2060 2070 2080 2090 2100 VELESKSIYK GVRDYNGIST IVCQLTNDSD RLKETMYGIG YGPIIITNGH LFRKNNGTIL 2110 2120 2130 2140 2150 2160 VRSWHGEFTV KNTTTLKVHF IEGKDVVLVR MPKTFPPFKS NASFRAPKRE ERACLVGTNF 2170 2180 2190 2200 2210 2220 QEKSLRSTVS ESSMTNPRRT GSYWIHWIST NEGDCGLPMV STTDGKLIGL HGKASTVSSK 2230 2240 2250 2260 2270 2280 NYFVPFTDDF MATHLSKLDD LTWTQHWLWQ PSKIAWGLLN LVDEQPGPEF RISNLVKDLF 2290 2300 2310 2320 2330 2340 NSGVETQSKR ERWVYESCEG NLRAVGSAQS ALVTKHVVKG KCPFFEEYLQ THAEASAYFR 2350 2360 2370 2380 2390 2400 PLMGEYQPSK LNKEAFKKDF FKYNKPVIVN QLDHDKFLEA VDGVIRMMCD FEFNECRFIT 2410 2420 2430 2440 2450 2460 DPEEIYSSLN MKAAIGAQYR GKKKEYFEGL DNFDMERLLF QSCERLFNGY KGLWNGSLKA 2470 2480 2490 2500 2510 2520 ELRPLEKVQA NKTRTFTAAP IDTLLGAKVC VDDFNNEFYS KNLKCPWTVG MSKFYGGWDK 2530 2540 2550 2560 2570 2580 LMRALPDGWL YCHADGSQFD SSLTPALLNA VLIIRSFYME DWWVGQEMLE NLYAEIVYTP 2590 2600 2610 2620 2630 2640 ILAPDGTIFK KFRGNNSGQP STVVDNTLMV VISIYYACIK FGWGYDEIEN RLVFFANGDD 2650 2660 2670 2680 2690 2700 LILAVKDEDS GLLDNMSASF SELGLNYDFS ERTHKREDLW FMSHQAMLVD GMYIPKLERE 2710 2720 2730 2740 2750 2760 RIVSILEWDR SKEVMHRTEA ICAAMIEAWG HTELLHEIRK FYLWFVEKEE VRELAALGKA 2770 2780 2790 2800 2810 2820 PYIAETALRK LYTDKGAETS ELARYLQALH QDVFFEQRDT VMLQSDTQTK EADAGAAKRD 2830 2840 2850 2860 2870 2880 KDEEKEKKKD VASSSANEKT MTATAKDKDV NAGSHGKIVP RLSKITKKMS LPRVKGSVIL 2890 2900 2910 2920 2930 2940 DIDHLLEYKP DQIELYNTRA SHQQFASWFN QVKAEYDLNE QQMGVVMNGF MVWCIENGTS 2950 2960 2970 2980 2990 3000 PDINGVWFMM DGDEQVEYPL KPIVENAKPT LRQIMHHFSD AAEAYIEMRN AEAPYMPRYG 3010 3020 3030 3040 3050 3060 LLRNLRDRSL ARYAFDFYEV NSKTPDRARE AVAQMKAAAL SNVSSRLFGL DGNVATNSED 3070 3080 TERHTARDVN RNMHTLLGVN TMQ

References

[1]	"Characterization of the P1 protein and coding region of the zucchini yellow mosaic virus." Wisler G.C., Purcifull D.E., Hiebert E. J. Gen. Virol. 76:37-45(1995) [PubMed: 7844540] [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	L29569 Genomic RNA. Translation: AAA65558.1.
3D structure databases
ProteinModelPortal	Q89330.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR014001. DEAD-like_helicase. IPR011492. DEAD_Flavivir. 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	PF07652. Flavi_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_ZYMVR

Accession

Primary (citable) accession number: Q89330

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 1998
Last sequence update:	November 1, 1996
Last modified:	November 16, 2011
This is version 98 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program