Reviewed, UniProtKB/Swiss-Prot P18479 (POLG_ZYMVC)

Names and origin

Protein names	Recommended name:     Genome polyprotein Cleaved into the following 10 chains:     1- Recommended name:             P1 proteinase         Alternative name(s):             N-terminal protein     2- Recommended name:             Helper component proteinase                 Short name=HC-pro               EC=3.4.22.45     3- Recommended name:             Protein P3     4- Recommended name:             6 kDa protein 1                 Short name=6K1     5- Recommended name:             Cytoplasmic inclusion protein                 Short name=CI               EC=3.6.1.-     6- Recommended name:             6 kDa protein 2                 Short name=6K2     7- Recommended name:             Viral genome-linked protein         Alternative name(s):             VPg     8- Recommended name:             Nuclear inclusion protein A                 Short name=NI-a                 Short name=NIa               EC=3.4.22.44         Alternative name(s):             NIa-pro             49 kDa proteinase               Short name=49 kDa-Pro     9- Recommended name:             Nuclear inclusion protein B                 Short name=NI-b                 Short name=NIb               EC=2.7.7.48         Alternative name(s):             RNA-directed RNA polymerase     10- Recommended name:             Coat protein                 Short name=CP
Organism	Zucchini yellow mosaic virus (strain California) (ZYMV) [Complete proteome]
Taxonomic identifier	117128 [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	3080 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	Coat 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. Ref.3 Nuclear inclusion protein B is a RNA-dependent RNA polymerase that plays an essential role in the virus replication. Ref.3 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. Ref.3 Cytoplasmic inclusion protein has helicase activity. It may be involved in replication By similarity. Ref.3 Both 6K peptides are indispensable for virus replication By similarity. Ref.3 Nuclear inclusion protein A has RNA-binding and proteolytic activities. Ref.3
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	Coat 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	Capsid protein Virion
Ligand	ATP-binding Nucleotide-binding
Molecular function	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: InterPro transcription, RNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW 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 – 310	310	P1 proteinase Potential		PRO_0000040500
	Chain	311 – 766	456	Helper component proteinase Potential		PRO_0000040501
	Chain	767 – 1112	346	Protein P3 By similarity		PRO_0000040502
	Chain	1113 – 1164	52	6 kDa protein 1 By similarity		PRO_0000040503
	Chain	1165 – 1798	634	Cytoplasmic inclusion protein By similarity		PRO_0000040504
	Chain	1799 – 1851	53	6 kDa protein 2 By similarity		PRO_0000040505
	Chain	1852 – 2041	190	Viral genome-linked protein By similarity		PRO_0000040506
	Chain	2042 – 2284	243	Nuclear inclusion protein A By similarity		PRO_0000040507
	Chain	2285 – 2801	517	Nuclear inclusion protein B By similarity		PRO_0000040508
	Chain	2802 – 3080	279	Coat protein By similarity		PRO_0000040509
Regions
	Domain	1236 – 1388	153	Helicase ATP-binding
	Domain	1407 – 1566	160	Helicase C-terminal
	Domain	2526 – 2650	125	RdRp catalytic
	Nucleotide binding	1249 – 1256	8	ATP Potential
	Motif	362 – 365	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	618 – 620	3	Involved in virions binding and aphid transmission
	Motif	1338 – 1341	4	DECH box
	Motif	1891 – 1900	10	Nuclear localization signal Potential
Sites
	Active site	652	1	For helper component proteinase activity By similarity
	Active site	725	1	For helper component proteinase activity By similarity
	Active site	2087	1	For nuclear inclusion protein A activity By similarity
	Active site	2122	1	For nuclear inclusion protein A activity By similarity
	Active site	2192	1	For nuclear inclusion protein A activity By similarity
	Site	310 – 311	2	Cleavage; by P1 proteinase Potential
	Site	766 – 767	2	Cleavage; by HC-pro Potential
	Site	1112 – 1113	2	Cleavage; by NIa-pro By similarity
	Site	1164 – 1165	2	Cleavage; by NIa-pro By similarity
	Site	1798 – 1799	2	Cleavage; by NIa-pro By similarity
	Site	2041 – 2042	2	Cleavage; by NIa-pro By similarity
	Site	2284 – 2285	2	Cleavage; by NIa-pro By similarity
	Site	2801 – 2802	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1915	1	O-(5'-phospho-RNA)-tyrosine By similarity
Experimental info
	Mutagenesis	618	1	P → A: Complete loss of aphid transmission and binding to virions. Ref.3
	Mutagenesis	619	1	T → A: Complete loss of aphid transmission and binding to virions. Ref.3
	Mutagenesis	619	1	T → S or V: Strongly reduced aphid transmission and binding to virions. Ref.3
	Mutagenesis	620	1	K → E: Slightly reduced aphid transmission and binding to virions. Ref.3
	Sequence conflict	2694 – 2695	2	LE → ST in AAA48511. Ref.2
	Sequence conflict	2699 – 2701	3	IVS → LFP in AAA48511. Ref.2
	Sequence conflict	2811	1	A → T in AAA48511. Ref.2
	Sequence conflict	2834	1	G → S in AAA48511. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P18479-1 [UniParc]. Last modified December 15, 1998. Version 2. Checksum: 2A1E501DEA6B9F73	FASTA	3,080	350,629
	10 20 30 40 50 60 MASIMIGSIS VPIAKTEQCA NTQVSNRANI VAPGHMATCP LPLKTHMYYR HESKKLMQSN 70 80 90 100 110 120 KSIDILNNFF STDEMKFRLT RNEMSKLKKG PSGRIVLRKP SKQRVFARIE QDEAARKEEA 130 140 150 160 170 180 VFLEGNYDDS ITNLARVLPP AVTHNVDVSL RSPFYKRTYK KERKKVAQKQ IVQAPLNSLC 190 200 210 220 230 240 TRVLKIARNK NIPVEMIGNK KTRHTLTFKR FRGCFVGKVS VAHEEGRMRH TEMSYEQFKW 250 260 270 280 290 300 LLKAICQVTH TERIREEDIK PGCSGWVLGT NHTLTKRYSR LPHLVIRGRD DDGIVNALEQ 310 320 330 340 350 360 VLFYSEVDHS SSQPEVQFFQ GWRRIFDKFR PSPDHVCKAD HNNEECGELA AIFCQALFPV 370 380 390 400 410 420 VKLSCQTCRE SLVEVSFEEF KDSLNANFII HKDEWGSFKE GSQYDNIFKL IKVATQATQN 430 440 450 460 470 480 LKLSSEVMKL VQNHTSTHMK QIQDINKALM KGSLVAQDEL DLALKQLLEM TQWFKNHMHL 490 500 510 520 530 540 TGEEALKMFR NKRSSKAMIN PSLLCGNQLD KNGNFVWGER GYHSKRLFKN FFEEVIPSEG 550 560 570 580 590 600 YTKYVVRNFP NGTRKLAIGS LIVPLNLDRA RTALLGESIE KKPLTSACVS QQNGNYIHSC 610 620 630 640 650 660 CCVTMDDGTP MYSELKSPTK RHLVIGASSD PKYIDLPASE AERMYIAKEG YCYLSIFLAM 670 680 690 700 710 720 LVNVNENEAK DFTKMIRDVL IPMLGQWPSL MDVATAAYIL GVFHPETRCA ELPRILVDHA 730 740 750 760 770 780 TQTMHVIDSY GSLTVGYHVL KAGTVNHLIQ FASNDLQSEM KHYRVGGTPT QRIKLEEQLI 790 800 810 820 830 840 KGIFKPKLMM QLLHDDPYIL LLGMISPTIL VHMYRMRHFE RGIEIWIKRD HEIGKIFVIL 850 860 870 880 890 900 EQLTRKVALA EVLVDQLNLI SEASPHLLEI MKGCQDNQRA YVPALDLLTI QVEREFSNKE 910 920 930 940 950 960 LKTNGYPDLQ QTLFDMREKM YAKQLHNSWQ ELSLLEKSCV TVRLKQFSIF TERNLIQRAK 970 980 990 1000 1010 1020 EGKRASSLQF VHECFITTRV HAKSIRDAGV RKLNEALVGT CKFFFSCGFK IFARCYSDII 1030 1040 1050 1060 1070 1080 YLVNVCLVFS LVLQMSNTVR SMIAATREEK ERAMANKADE NERTLMHMYH IFSKKQDDAP 1090 1100 1110 1120 1130 1140 IYNDFLEHVR NVRPDLEETL LYMAGVEVVS TQAKSAVQIQ FEKIIAVLAL LTMCFDAERS 1150 1160 1170 1180 1190 1200 DAIFKILTKL KTVFGTVGET VRLQGLEDIE SLEDDKRLTI DFDINTNEAH SSTTFDVHFD 1210 1220 1230 1240 1250 1260 DWWNRQLQQN RTVPHYRTTG KFLEFTRNTA AFVANEIASS SEGEFLVRGR VGSGKSTSLP 1270 1280 1290 1300 1310 1320 AHLAKKGKVL LLEPTRPLAE NVSRQLAGDP FFQNVTLRMR GLSCFGSSNI TVMTSGFAFH 1330 1340 1350 1360 1370 1380 YYVNNPHQLM EFDFVIIDEC HVTDSATIAF NCALKEYNFA GKLIKVSATP PGRECDFDTQ 1390 1400 1410 1420 1430 1440 FAVKVKTEDH LSFHAFVGAQ KTGSNADMVQ HGNNILVYVA SYNEVDMLSK LLTERQFSVT 1450 1460 1470 1480 1490 1500 KVDGRTMQLG KTTIETHGTS QKPHFIVATN IIENGVTLDV ECVVDFGLKV GRRTGQRNRC 1510 1520 1530 1540 1550 1560 VRYNKKSVSY GERIQRLGRV GRSKPGTALR IGHTEKGIET IPEFIATEAA ALSFAYGLPV 1570 1580 1590 1600 1610 1620 TTHGVSTNIL GKCTVKQMKC ALNFELTPFF TTHLIRHDGS MHPLIHEELK QFKLRDSEMV 1630 1640 1650 1660 1670 1680 LNKVALPHQF VSQWMDQSEY ERIGVHVQCH ESNSIPFYTN GIPDKVYERI WKCIQENKND 1690 1700 1710 1720 1730 1740 AVFGKLSSAC STKVSYTLST DPAALPRTIA IIDHLLAEEM MKRNHFDTIS SAVTGYSFSL 1750 1760 1770 1780 1790 1800 AGIADSFRKR YMRDYTAHNI AILQQARAQL LEFNSKNVNI NNLSDLEGIG VIKSVVLQSK 1810 1820 1830 1840 1850 1860 QEVSSFLGLR GKWDGKKFAN DVILAIMTLL GGGWFMWEYF TKKINEPVRV ESKKRRSQKL 1870 1880 1890 1900 1910 1920 KFRDAYDRKV GREIFGDDDT IGRTFGEAYT KRGKVKGNNN TKGMGRKTRN FVHLYGVEPE 1930 1940 1950 1960 1970 1980 NYSFIRFVDP LTGHTLDEST HTDISLVQEE FGSIREKFLE NDLISRQSII NKPGIQAYFM 1990 2000 2010 2020 2030 2040 GKGTEEALKV DLTPHVPLLL CRNTNAIAGY PERENELRQT GTPVKVSFKD VPEKNEHVEL 2050 2060 2070 2080 2090 2100 ESKSIYKGVR DYNGISTIVC QLTNDSDGLK ETMYGIGYGP IIITNGHLFR KNNGTLLVRS 2110 2120 2130 2140 2150 2160 WHGEFIVKNT TTLKVHFIEG KDVVLVRMPK DFPPFKSNAS FRAPKREERR CLVGTNFQEK 2170 2180 2190 2200 2210 2220 SLRSTVSESS MTIPEGTGSY WIHWISTNEG DCGLPMVSTT DGKIIGVHGL ASTVSSKNYF 2230 2240 2250 2260 2270 2280 VPFTDDFIAT HLSKLDDLTW TQHWLWQPSK IAWGTLNLVD EQPGPEFRIS NLVKDLFTSG 2290 2300 2310 2320 2330 2340 VETQSKRERW VYESCEGNLR AVGTAQSALV TKHVVKGKCP FFEEYLQTHA EASAYFRPLM 2350 2360 2370 2380 2390 2400 GEYQPSKLNK EAFKKDFFKY NKPVTVNQLD HDKFLGAVDG VIRMMCDFEF NECRFITDPE 2410 2420 2430 2440 2450 2460 EIYNSLNMKA AIGAQYRGKK KEYFEGLDDF DRERLLFQSC ERLFNGYKGL WNGSLKAELR 2470 2480 2490 2500 2510 2520 PLEKVRANKT RTFTAAPIDT LLGAKVCVDD FNNEFYRKNL KCPWTVGMTK FYGGWDKLMR 2530 2540 2550 2560 2570 2580 SLPDGWLYCH ADGSQFDSSL TPALLNAVLI IRSFYMEDWW VGQEMLENLY AEIVYTPILA 2590 2600 2610 2620 2630 2640 PDGTIFKKFR GNNSGQPSTV VDNTLMVVIS IYYACMKFGW NCEEIENKLV FFANGDDLIL 2650 2660 2670 2680 2690 2700 AVKDEDSGLL DNMSSSFCEL GLNYDFSERT HKREDLWFMS HQAMLVDGMY TPKLEKERIV 2710 2720 2730 2740 2750 2760 SILEWDRSKE IMHRTEAICA AMIEAWGHTE LLQEIRKFYL WFVEKEEVRE LAALGKAPYI 2770 2780 2790 2800 2810 2820 AETALRKLYT DKGADTSELA RYLQALHQDI FFEQGDTVML QSGTQPTVAD AGATKKDKED 2830 2840 2850 2860 2870 2880 DKGKNKDVTG SGSGEKTVAA VTKDKDVNAG SHGKIVPRLS KITKKMSLPR VKGNVILDID 2890 2900 2910 2920 2930 2940 HLLEYKPDQI ELYNTRASHQ QFASWFNQVK TEYDLNEQQM GVVMNGFMVW CIENGTSPDI 2950 2960 2970 2980 2990 3000 NGVWVMMDGN EQVEYPLKPI VENAKPTLRQ IMHHFSDAAE AYIEMRNAEA PYMPRYGLLR 3010 3020 3030 3040 3050 3060 NLRDRSLARY AFDFYEVNSK TPERAREAVA QMKAAALSNV SSRLFGLDGN VATTSEDTER 3070 3080 HTARDVNRNM HTLLGVNTMQ

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]	"Nucleotide sequence of the zucchini yellow mosaic virus capsid-encoding gene and its expression in Escherichia coli." Gal-On A., Antignus Y., Rosner A., Raccah B. Gene 87:273-277(1990) [PubMed: 2185142] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2694-3080.
[3]	"Mutations in the HC-Pro gene of zucchini yellow mosaic potyvirus: effects on aphid transmission and binding to purified virions." Peng Y.H., Kadoury D., Gal-On A., Huet H., Wang Y., Raccah B. J. Gen. Virol. 79:897-904(1998) [PubMed: 9568986] [Abstract] Cited for: FUNCTION OF HELPER COMPONENT PROTEINASE, MUTAGENESIS OF PRO-618; THR-619 AND LYS-620.
[4]	"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	L31350 Genomic RNA. Translation: AAA65559.1. M35095 Genomic RNA. Translation: AAA48511.1.
PIR	JH0103.
3D structure databases
SMR	P18479. Positions 2049-2263.
ModBase	Search...
Family and domain databases
InterPro	IPR014001. DEAD-like_N. IPR001650. DNA/RNA_helicase_C. IPR014021. Helicase_SF1/SF2_ATP-bd. 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. IPR009003. Ser/Cys_Pept_Trypsin-like. [Graphical view]
Pfam	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]
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_ZYMVC

Accession

Primary (citable) accession number: P18479
Secondary accession number(s): Q89334

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	December 15, 1998
Last modified:	February 9, 2010
This is version 90 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)