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Protein

Genome polyprotein

Gene
N/A
Organism
Zucchini yellow mosaic virus (strain Reunion Island) (ZYMV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

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.
Nuclear inclusion protein B: an RNA-dependent RNA polymerase that plays an essential role in the virus replication.
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).By similarity
Cytoplasmic inclusion protein: has helicase activity. It may be involved in replication (By similarity).By similarity
Both 6K peptides are indispensable for virus replication.By similarity
Nuclear inclusion protein A: has RNA-binding and proteolytic activities.

Catalytic activityi

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).PROSITE-ProRule annotation
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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei267 – 2671For P1 proteinase activityBy similarity
Active sitei655 – 6551For helper component proteinase activityPROSITE-ProRule annotation
Active sitei728 – 7281For helper component proteinase activityPROSITE-ProRule annotation
Active sitei2090 – 20901For nuclear inclusion protein A activityPROSITE-ProRule annotation
Active sitei2125 – 21251For nuclear inclusion protein A activityPROSITE-ProRule annotation
Active sitei2195 – 21951For nuclear inclusion protein A activityPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1252 – 12598ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Suppressor of RNA silencing, Thiol protease, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 10 chains:
Alternative name(s):
N-terminal protein
Helper component proteinase (EC:3.4.22.45)
Short name:
HC-pro
6 kDa protein 1
Short name:
6K1
6 kDa protein 2
Short name:
6K2
Alternative name(s):
VPg
Nuclear inclusion protein A (EC:3.4.22.44)
Short name:
NI-a
Short name:
NIa
Alternative name(s):
49 kDa proteinase
Short name:
49 kDa-Pro
NIa-pro
Nuclear inclusion protein B (EC:2.7.7.48)
Short name:
NI-b
Short name:
NIb
Alternative name(s):
RNA-directed RNA polymerase
Capsid protein
Short name:
CP
Alternative name(s):
Coat protein
OrganismiZucchini yellow mosaic virus (strain Reunion Island) (ZYMV)
Taxonomic identifieri117129 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stagePotyviridaePotyvirus
Virus hostiCitrullus lanatus (Watermelon) (Citrullus vulgaris) [TaxID: 3654]
Cucumis melo (Muskmelon) [TaxID: 3656]
Cucumis sativus (Cucumber) [TaxID: 3659]
Cucurbita pepo (Vegetable marrow) (Summer squash) [TaxID: 3663]
Proteomesi
  • UP000008611 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Helical capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 30833083Genome polyproteinPRO_0000420036Add
BLAST
Chaini1 – 313313P1 proteinaseSequence analysisPRO_0000040510Add
BLAST
Chaini314 – 769456Helper component proteinaseSequence analysisPRO_0000040511Add
BLAST
Chaini770 – 1115346Protein P3By similarityPRO_0000040512Add
BLAST
Chaini1116 – 1167526 kDa protein 1By similarityPRO_0000040513Add
BLAST
Chaini1168 – 1801634Cytoplasmic inclusion proteinBy similarityPRO_0000040514Add
BLAST
Chaini1802 – 1854536 kDa protein 2By similarityPRO_0000040515Add
BLAST
Chaini1855 – 2044190Viral genome-linked proteinBy similarityPRO_0000040516Add
BLAST
Chaini2045 – 2287243Nuclear inclusion protein ABy similarityPRO_0000040517Add
BLAST
Chaini2288 – 2804517Nuclear inclusion protein BBy similarityPRO_0000040518Add
BLAST
Chaini2805 – 3083279Capsid proteinBy similarityPRO_0000040519Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1918 – 19181O-(5'-phospho-RNA)-tyrosineBy similarity

Post-translational modificationi

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).By similarity
Potyviral RNA is expressed as two polyproteins which undergo post-translational proteolytic processing. Genome polyprotein is processed by NIa-pro, P1 and HC-pro proteinases resulting in the production of at least ten individual proteins. P3N-PIPO polyprotein is cleaved by P1 and HC-pro proteinases resulting in the production of three 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).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei313 – 3142Cleavage; by P1 proteinaseSequence analysis
Sitei769 – 7702Cleavage; by autolysisPROSITE-ProRule annotation
Sitei1115 – 11162Cleavage; by NIa-proBy similarity
Sitei1167 – 11682Cleavage; by NIa-proBy similarity
Sitei1801 – 18022Cleavage; by NIa-proBy similarity
Sitei2044 – 20452Cleavage; by NIa-proBy similarity
Sitei2287 – 22882Cleavage; by NIa-proBy similarity
Sitei2804 – 28052Cleavage; by NIa-proBy similarity

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Structurei

3D structure databases

ProteinModelPortaliQ89330.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini647 – 769123Peptidase C6PROSITE-ProRule annotationAdd
BLAST
Domaini1239 – 1391153Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini1410 – 1569160Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST
Domaini2045 – 2263219Peptidase C4PROSITE-ProRule annotationAdd
BLAST
Domaini2529 – 2653125RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi365 – 3684Involved in interaction with stylet and aphid transmissionBy similarity
Motifi621 – 6233Involved in virions binding and aphid transmissionBy similarity
Motifi1341 – 13444DECH box
Motifi1894 – 190310Nuclear localization signalSequence analysis

Domaini

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.

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation
Contains 1 peptidase C4 domain.PROSITE-ProRule annotation
Contains 1 peptidase C6 domain.PROSITE-ProRule annotationCurated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011492. DEAD_Flavivir.
IPR001456. HC-pro.
IPR031159. HC_PRO_CPD_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR009003. Peptidase_S1_PA.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[Graphical view]
PfamiPF07652. 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]
PRINTSiPR00966. NIAPOTYPTASE.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51744. HC_PRO_CPD. 1 hit.
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]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Isoform Genome polyprotein (identifier: Q89330-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAAIMIGSIS VPIVESARCA TVQTGNRVNI VAPGHVAVCK PQMKSHSYYK
60 70 80 90 100
HASEKLSKQA SESINILNSF FDTDPEMRFR LTRNEMSKVK KGPNGRMILR
110 120 130 140 150
KPRAQRVLER ISFEKIEKGA ERQVLPWRVY ATVTSIINTF TDERNGIANS
160 170 180 190 200
SLRSPFYKRS CRKEKKKIVC ENVVRSASVN NLCDRVLKIA REKNIPVEMI
210 220 230 240 250
GKKKNRHTLT FKNFKGSFIG KVSLAHERGQ MRHVEMSYEQ FGFILQAICR
260 270 280 290 300
VTNTRCVRDE DIKPGCSGWV LGDDHELTQK FSRLPCLVIR GRDDEGIVNA
310 320 330 340 350
LEPVFFYDDV DHYSSQPEVQ FFQGWRRMFD NFKPSSDHVC KVDHGNEECG
360 370 380 390 400
ELAAIFSQAL FPVVKLSCQT CREKLSRVSF EEFKDSLAIN FTVHKSEWDS
410 420 430 440 450
LKENPHHDNV LKLIKGATQA TQNLKLSSEV MKLVQNHTST HMKQIQDINR
460 470 480 490 500
ALMKGSLVTQ DELDLALKQL LEMTQWFKNH MHLTGEEALK TFRNKRSSKA
510 520 530 540 550
MINPSLLCDN QLDKNGNFVW GERGYHSKRL FKNFFEEVIP SEGYTKYIVR
560 570 580 590 600
NFPNGTRKLA IGSLIVPLNL DRARTALLGE SIEKEPLTSA CVSQQNGNYI
610 620 630 640 650
HSCCCVTMDD GTPMYSDVKS PTKRHLVIGA SGDPKYIDLP ASEADRMYIA
660 670 680 690 700
KEGYCYLNIF LAMLVNVNEN EAKDFTKMIR DVLIPMLGQW PSLMDVATAA
710 720 730 740 750
YILGVFHPET RCAELPRILV DHATQTMHVI DSYGSLTVGY HVLKAGTVNH
760 770 780 790 800
LIQFASNDLQ SEMKHYRVGG TPTQRIKLEE QLIKGIFKPK LMMQLLQDDP
810 820 830 840 850
YVLILGMVSP TILVHMYRMR HFERGIEMWI KRDHEVGKIF VILEQLTRKV
860 870 880 890 900
ALTEVLVDQL DLISEASPHL LEIMKGCQDN QRAYVPALDL LTVQVEREFS
910 920 930 940 950
NKELKVNGYP DLQQTLYDMR EKIYAKQLHD SWQELSLLEK SCVTVRLKRF
960 970 980 990 1000
SIFTERKLTQ QAKDGKRVSS LQFVHECFIT TRVHAKSIRD VGMRKFNEAL
1010 1020 1030 1040 1050
VGTCKFLFTC GFKIFARCYS DIIYLVNVCL IFSLVLQMSN TVRSMISATR
1060 1070 1080 1090 1100
EEKERALANK ADENERTLMH MYHIFSKKQD DAPLYSEFLE HVRNVRPDLE
1110 1120 1130 1140 1150
ETLLYMAGAE IVTPQAKSAV QVQFEKIIAV VALLTMCFDA ERSDAIFKIL
1160 1170 1180 1190 1200
TKLKTVFGTV GETVRLQGLE DIENLEDDKK LTIDFDINTN EAQSSTTFDV
1210 1220 1230 1240 1250
HFDDWWNRQL QQNRTVPHYR TTGKFLEFTR NTAAFVANEI ASSNEGEFLV
1260 1270 1280 1290 1300
RGAVGSGKST SLPAHLAKKG KVLLLEPTRP LAENVSRQLA GDPFFQNVTL
1310 1320 1330 1340 1350
RMRGLSCFGS SNITVMTSGY AFHYYVNNPH QMMEFDFIII DECHVTDSAT
1360 1370 1380 1390 1400
IAFNCALKEY NFAGKLIKVS ATPPGRECDF DTQFAVKVKT EDHLSFQAFV
1410 1420 1430 1440 1450
GAQRTGSNAD MIQHGNNILV YVASYNEVDM LSKLLTERQF SVTKVDGRTM
1460 1470 1480 1490 1500
QLGKTTIETH GTSQKPHFIV ATNIIENGVT LDVDCVVDFG LKVVAELDSE
1510 1520 1530 1540 1550
SRCVRYSKKP VNYGERIQRL GRVGRSKPGT ALRIGHTEKG IENIPEFIAT
1560 1570 1580 1590 1600
EAAALSFAYG LSVTTHGVST NILGKCTVKQ MKCALNFELT PFFTTHLIRH
1610 1620 1630 1640 1650
DGSMHPLIHE ELKQFKLRDS EMVLNKVALP HQFVSQWMTQ GDYEHIGVHI
1660 1670 1680 1690 1700
QCNENTRIPF YTNGIPDRVY EKIWKCIQEN KNDALFGRLS SACSTKVSYT
1710 1720 1730 1740 1750
LSTDPAALPR TIAIIDHLLA EEMMKRNHFD MISSAVTGYS FSLAGIADSF
1760 1770 1780 1790 1800
RKRYMRDHTA HNIAILQQAR AQLLEFDSKN VNINNLSDLE GIGVIKSVVL
1810 1820 1830 1840 1850
QSKQEVSNFL GLRGKWDGRK FANDVILAIM TLLGGGWFMW EYFTKKVNEP
1860 1870 1880 1890 1900
VRVESKKRRS QKLKFRDAYD RKVGREIFGD DETIGRTFGE AYTKRGKVKG
1910 1920 1930 1940 1950
NNSTKGMGRK TRNFVHLYGV EPENYSFIRF VDPLTGHTLD ESTHTDISLV
1960 1970 1980 1990 2000
QEEFGNIREK FLENDLISRQ SIINKPGIQA YFMGKGTAEA LKFDFTPHVP
2010 2020 2030 2040 2050
SLSCSNSNAH AGYPERENEL RQTGTPVKVS LKDVPEKNEH VELESKSIYK
2060 2070 2080 2090 2100
GVRDYNGIST IVCQLTNDSD RLKETMYGIG YGPIIITNGH LFRKNNGTIL
2110 2120 2130 2140 2150
VRSWHGEFTV KNTTTLKVHF IEGKDVVLVR MPKTFPPFKS NASFRAPKRE
2160 2170 2180 2190 2200
ERACLVGTNF QEKSLRSTVS ESSMTNPRRT GSYWIHWIST NEGDCGLPMV
2210 2220 2230 2240 2250
STTDGKLIGL HGKASTVSSK NYFVPFTDDF MATHLSKLDD LTWTQHWLWQ
2260 2270 2280 2290 2300
PSKIAWGLLN LVDEQPGPEF RISNLVKDLF NSGVETQSKR ERWVYESCEG
2310 2320 2330 2340 2350
NLRAVGSAQS ALVTKHVVKG KCPFFEEYLQ THAEASAYFR PLMGEYQPSK
2360 2370 2380 2390 2400
LNKEAFKKDF FKYNKPVIVN QLDHDKFLEA VDGVIRMMCD FEFNECRFIT
2410 2420 2430 2440 2450
DPEEIYSSLN MKAAIGAQYR GKKKEYFEGL DNFDMERLLF QSCERLFNGY
2460 2470 2480 2490 2500
KGLWNGSLKA ELRPLEKVQA NKTRTFTAAP IDTLLGAKVC VDDFNNEFYS
2510 2520 2530 2540 2550
KNLKCPWTVG MSKFYGGWDK LMRALPDGWL YCHADGSQFD SSLTPALLNA
2560 2570 2580 2590 2600
VLIIRSFYME DWWVGQEMLE NLYAEIVYTP ILAPDGTIFK KFRGNNSGQP
2610 2620 2630 2640 2650
STVVDNTLMV VISIYYACIK FGWGYDEIEN RLVFFANGDD LILAVKDEDS
2660 2670 2680 2690 2700
GLLDNMSASF SELGLNYDFS ERTHKREDLW FMSHQAMLVD GMYIPKLERE
2710 2720 2730 2740 2750
RIVSILEWDR SKEVMHRTEA ICAAMIEAWG HTELLHEIRK FYLWFVEKEE
2760 2770 2780 2790 2800
VRELAALGKA PYIAETALRK LYTDKGAETS ELARYLQALH QDVFFEQRDT
2810 2820 2830 2840 2850
VMLQSDTQTK EADAGAAKRD KDEEKEKKKD VASSSANEKT MTATAKDKDV
2860 2870 2880 2890 2900
NAGSHGKIVP RLSKITKKMS LPRVKGSVIL DIDHLLEYKP DQIELYNTRA
2910 2920 2930 2940 2950
SHQQFASWFN QVKAEYDLNE QQMGVVMNGF MVWCIENGTS PDINGVWFMM
2960 2970 2980 2990 3000
DGDEQVEYPL KPIVENAKPT LRQIMHHFSD AAEAYIEMRN AEAPYMPRYG
3010 3020 3030 3040 3050
LLRNLRDRSL ARYAFDFYEV NSKTPDRARE AVAQMKAAAL SNVSSRLFGL
3060 3070 3080
DGNVATNSED TERHTARDVN RNMHTLLGVN TMQ
Note: Produced by conventional translation.
Length:3,083
Mass (Da):351,161
Last modified:November 1, 1996 - v1
Checksum:i55E51B455C20C537
GO
Isoform P3N-PIPO polyprotein (identifier: P0CK14-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0CK14.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by -1 ribosomal frameshifting in P3 ORF.
Length:996
Mass (Da):113,760
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L29569 Genomic RNA. Translation: AAA65558.1.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L29569 Genomic RNA. Translation: AAA65558.1.

3D structure databases

ProteinModelPortaliQ89330.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011492. DEAD_Flavivir.
IPR001456. HC-pro.
IPR031159. HC_PRO_CPD_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR009003. Peptidase_S1_PA.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
[Graphical view]
PfamiPF07652. 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]
PRINTSiPR00966. NIAPOTYPTASE.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51744. HC_PRO_CPD. 1 hit.
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]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_ZYMVR
AccessioniPrimary (citable) accession number: Q89330
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.