Reviewed, UniProtKB/Swiss-Prot O36979 (POLG_ZYMVS)

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 Singapore) (ZYMV) [Complete proteome]
Taxonomic identifier	117130 [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	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. 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	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 – 314	314	P1 proteinase Potential		PRO_0000040520
	Chain	315 – 769	455	Helper component proteinase Potential		PRO_0000040521
	Chain	770 – 1115	346	Protein P3 By similarity		PRO_0000040522
	Chain	1116 – 1167	52	6 kDa protein 1 By similarity		PRO_0000040523
	Chain	1168 – 1801	634	Cytoplasmic inclusion protein By similarity		PRO_0000040524
	Chain	1802 – 1854	53	6 kDa protein 2 By similarity		PRO_0000040525
	Chain	1855 – 2044	190	Viral genome-linked protein By similarity		PRO_0000040526
	Chain	2045 – 2287	243	Nuclear inclusion protein A By similarity		PRO_0000040527
	Chain	2288 – 2804	517	Nuclear inclusion protein B By similarity		PRO_0000040528
	Chain	2805 – 3083	279	Coat protein By similarity		PRO_0000040529
Regions
	Domain	1239 – 1391	153	Helicase ATP-binding
	Domain	1410 – 1569	160	Helicase C-terminal
	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	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)
	O36979-1 [UniParc]. Last modified December 19, 2001. Version 2. Checksum: B4B6C53C14524A88	FASTA	3,083	351,033
	10 20 30 40 50 60 MAAIMIGSIS VPIIGSAQCA TAPIGNRVNI VAPGHMAICK PQMRSHAYYK HASQKLSEQS 70 80 90 100 110 120 SRGIEVLNSF FNNDPEDAFR LTRNGMSKVK KGPNGRIILR KPKARHVFER INLEKSEKEQ 130 140 150 160 170 180 KGKFFNGEYD TTVTSIKGVT TSKENDLGAF SLRSPFYKRT CKKEKRRITR ENIVCVDDVN 190 200 210 220 230 240 NLCERILKIT RDKNIPVEII GKRRNHHTLT FKKFKGSFVG KVSLAPERSQ MKHVEMSYGQ 250 260 270 280 290 300 FDYILQAICR ITSTKHVRDE DIKPGCSGWV FSTDHALTQK YSRLPYLVIR GRDDDGIVNA 310 320 330 340 350 360 LEPVLFYSDV EHYSFQNEVQ FFNGWRKMFD KLKPHSDHTC KVDHNNEECG EMAAVLSQAI 370 380 390 400 410 420 FPVLKLSCQV CREKLSRVSF EEFKDFLSRN FMTHESEWST LRDGVHCDNV LKLIKGAVQT 430 440 450 460 470 480 TQNLKLSSDI MKLVQNHTST HMKQIQDINK ALMKGSLVTQ DELDLALKQL LEMTQWFKNH 490 500 510 520 530 540 MHLTGEEALK TFRNKRSNKA MINPSLLCDN QLDKNGNFIW GERGYHSKRL FKNFFEEVIP 550 560 570 580 590 600 SEGYTKYIVR NFPNGTRKLA IGSLIVPLNL DRARTALLGE SIEKEPLTSA CISQQNENYI 610 620 630 640 650 660 HSCCCVTMDD GTPMYSELKS PTKRHLVIGA SGDPKYIDLP ASEAERMYIA KEGYCYLNIF 670 680 690 700 710 720 LAMLVNVNEN EAKDFTKMIR DVLIPMLGQW PSLMDVATAA YILGVFHPET RCAELPRILV 730 740 750 760 770 780 DHATQTMHVI DSYGSLTVGY HVLKAGTVNH LIQFASNDLQ SEMKHYRVGG TPTQRIRLEE 790 800 810 820 830 840 QLIKGIFKPK IMMQLLHDDP YILLLGMISP TILVHMYRMR HFERGIEIWI KRDHEIGKIF 850 860 870 880 890 900 VILEQLTRKV ALAEILVDQL DLISEASPHL LEIMNGCQDN QRAYAPALDL LTIQVEREFS 910 920 930 940 950 960 NKELKTNGYP DLHQTLHDMR EKMYAKQLHN SWQELSLLEK SCVTVRLKQF SIFTERNLTQ 970 980 990 1000 1010 1020 RAKERKHASS LQFVHECFIT TRVHAKSIRD AGVRKLNEAL VGTCKFFFSC GFRIFARCYS 1030 1040 1050 1060 1070 1080 DIIYFVNVCL VFSLVLQMSN TVRNMIAATR EEKERAMANK ADENERTLMH MYHIFCKKQD 1090 1100 1110 1120 1130 1140 DAPIYNDFLE HVRSVRPDLE ETLLYMAGGE VVTAQAKSAV QIQFEKIIAV LALLTMCFDA 1150 1160 1170 1180 1190 1200 ERSDAIFKIL TKLKIVFGTV GETVRLQGLE DIENLEDDKR LTIDFDINTN EAQSSTTFDV 1210 1220 1230 1240 1250 1260 HFEDWWNRQL QQNRTVPHYR TTGKFLEFTR STAAYVANEI ASSSEGEFLV RGAVGSGKST 1270 1280 1290 1300 1310 1320 SLPAHLAKKG KVLLLEPTRP LAENVSRQLA GDPFFQNVTL RMRGLSCFGS SNITVMTSGF 1330 1340 1350 1360 1370 1380 AFHYYVNNPH QLMEFDFVII DECHVTDSAT IAFNCALKEY SFAGKLIKVS ATPPGRECDF 1390 1400 1410 1420 1430 1440 DTQFAVKVKT EDHLSFNAFV GAQKTGSNAD MVQHGNNILV YVASYNEVDM LSKLLTERQF 1450 1460 1470 1480 1490 1500 SVTKVDGRTM QLGKTTIETH GTSQKPHFIV ATNIIENGVT LDVECVVDFG LKVVAELDSE 1510 1520 1530 1540 1550 1560 KRCVRYSKKP VSYGERIQRL GRVGRSKPGT ALRIGHTEKG IENIPEFIAT EAAALSFAYG 1570 1580 1590 1600 1610 1620 LSVTTHGVST NNLGKCTVKQ MKCALNFELT PFFTTHLIRH DGSMHPLIHE ELKQFKLRDS 1630 1640 1650 1660 1670 1680 EMVLNKVALP HQFVSQWMDQ SEYERIGVHI QCHESTRIPF YTNGIPDKVY ERIWKCIQEN 1690 1700 1710 1720 1730 1740 KNDALFGKLS SAFPSKVSYT LSTDPAALPR TIAIIDHLLA EEMMKRNHFD MISSAVTGYS 1750 1760 1770 1780 1790 1800 FSLAGIADSF RKRYMRDHTA HHIAILQQAR AQLLEFNSKN VNINNLSDLE GIGVIKSVVL 1810 1820 1830 1840 1850 1860 QSKQEVSSFL GLRGKWDGRK FANDVILAVM TLFGGGWFMW EYFTKKVNEP VRVESKKRRS 1870 1880 1890 1900 1910 1920 QKLKFRDAYD RKVGREIFGD NDTIGRTFGE AYTKRGKVKG NNSTKGMGRK TRNFVHLYGV 1930 1940 1950 1960 1970 1980 EPEIYSFIRF VDPLTGHTLD ESTHTDISLV QEEFGNIREK FLENDLISRQ SIINKPGIQA 1990 2000 2010 2020 2030 2040 YFMGKGTEEA LKVDLTPHVP LLLCRNTNAI AGYPERENEL RQTGTPIKVS FKEVPEKNEH 2050 2060 2070 2080 2090 2100 VELESKSIYK GVRDYNGIST IVCQLTNDSD GLKETMYGIG YGPIIITNGH LFRKNNGTLL 2110 2120 2130 2140 2150 2160 VRSWHGEFTV KNTTTLKVHF IEGKDVVLVR MPKDFPPFRS NASFRAPKRE ERACLVGTNF 2170 2180 2190 2200 2210 2220 QEKSLRSTVS ESSMTIPEGT GSYWIHWIST NEGDCGLPMV STTDGKIIGI HGLASTVSSK 2230 2240 2250 2260 2270 2280 NYFVPFTDDL LTTHLSKLDD LTWTQHWLWQ PSKIAWGSLN LVDEQPGPEF RISNLVKDLL 2290 2300 2310 2320 2330 2340 TSGVETQSKR ERWVYESCEG NLRAVGSAQS ALVTKHVVKG KCPFFEEYLQ THAEANTYFR 2350 2360 2370 2380 2390 2400 PLMGEYQPSK LNKEAFKKDF FKYNKPVVVN QLDHDKFLGA VNGVIRMMCD FEFNECRFIT 2410 2420 2430 2440 2450 2460 DPEEIYDSLN MKAAIGAQYR GKKKEYFEGL DNFDRERLLF QSCERLFNGH KGLWNGSLKA 2470 2480 2490 2500 2510 2520 ELRPLEKVQA NKTRTFTAAP IDTLLGAKVC VDDFNNEFYS KNLKCPWTVG MTKFYGGWDK 2530 2540 2550 2560 2570 2580 LMRELPDGWL YCHADGSQFD SSLTPALLNA VLIIRSFYME DWWVGQEMLE NLYAEIVYTP 2590 2600 2610 2620 2630 2640 ILAPDGTIFK KFRGNNSGQP STVVDNTLMV VISIYYACMK FGWSYEEIEN KLVFFANGDD 2650 2660 2670 2680 2690 2700 LILAVKDEDS GLLDNMSASF SELGLNYDFS ERTHKREDLW FMSHQAMLVD GMYIPKLEKE 2710 2720 2730 2740 2750 2760 RIVSILEWDR SKEIMHRTEA ICAAMIEAWG HTDLLREIRK FYLWFVEKEE VRELATLGKA 2770 2780 2790 2800 2810 2820 PYIAETALRK LYTDKGAETG ELARYLQALH QDIFFEQGDT VMLQSDTQTR EAGAGASKKD 2830 2840 2850 2860 2870 2880 KDEDKDKKKD VASSSASEKA VATATKDKDV NAGSHGKIVP RLSKITKKMS LPRVKGSVIL 2890 2900 2910 2920 2930 2940 DIDHLLEYKP DQIELYNTRA SHQQFASWFN QVKAEYDLNE QQMGVVMNGF MVWCIENGTS 2950 2960 2970 2980 2990 3000 PDINGVWVMM DGNEQVEYPL KPIVENAKPT LRQIMHHFSD AAEAYIEMRN AEAPYMPRYG 3010 3020 3030 3040 3050 3060 LLRNLRDRSL ARYAFDFYEV NSKTPDRARE AVAQMKAAAL SNVSSRLFGL DGNVATTSED 3070 3080 TERHTARDVN RNMHTLLGVN TMQ

References

[1]	Lee K.C., Wong S.M. Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases 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	AF014811 Genomic RNA. Translation: AAB72004.2.
3D structure databases
SMR	O36979. Positions 2052-2266.
ModBase	Search...
Protein family/group databases
MEROPS	C06.001.
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_ZYMVS

Accession

Primary (citable) accession number: O36979

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1999
Last sequence update:	December 19, 2001
Last modified:	February 9, 2010
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)