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Protein

Genome polyprotein

Gene
N/A
Organism
Potato virus A (PVA)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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.
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)DescriptionActionsGraphical viewLength
Active sitei207For P1 proteinase activityBy similarity1
Active sitei216For P1 proteinase activitySequence analysis1
Active sitei249For P1 proteinase activityBy similarity1
Active sitei641For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei714For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei2077For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2112For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2182For nuclear inclusion protein A activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1239 – 1246ATPPROSITE-ProRule annotation8

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

Protein family/group databases

MEROPSiC04.014.

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
OrganismiPotato virus A (PVA)
Taxonomic identifieri12215 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stagePotyviridaePotyvirus
Virus hostiSolanum tuberosum (Potato) [TaxID: 4113]
Proteomesi
  • UP000008484 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)DescriptionActionsGraphical viewLength
ChainiPRO_00004200141 – 3059Genome polyproteinAdd BLAST3059
ChainiPRO_00000403851 – 298P1 proteinaseSequence analysisAdd BLAST298
ChainiPRO_0000040386299 – 755Helper component proteinaseSequence analysisAdd BLAST457
ChainiPRO_0000040387756 – 1102Protein P3Add BLAST347
ChainiPRO_00000403881103 – 11546 kDa protein 1Add BLAST52
ChainiPRO_00000403891155 – 1789Cytoplasmic inclusion proteinAdd BLAST635
ChainiPRO_00000403901790 – 18426 kDa protein 2Add BLAST53
ChainiPRO_00000403911843 – 2031Viral genome-linked proteinAdd BLAST189
ChainiPRO_00000403922032 – 2274Nuclear inclusion protein AAdd BLAST243
ChainiPRO_00000403932275 – 2790Nuclear inclusion protein BAdd BLAST516
ChainiPRO_00000403942791 – 3059Capsid proteinAdd BLAST269

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1905O-(5'-phospho-RNA)-tyrosineBy similarity1

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.
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)DescriptionActionsGraphical viewLength
Sitei298 – 299Cleavage; by P1 proteinaseSequence analysis2
Sitei755 – 756Cleavage; by autolysisPROSITE-ProRule annotation2
Sitei1102 – 1103Cleavage; by NIa-proBy similarity2
Sitei1154 – 1155Cleavage; by NIa-proBy similarity2
Sitei1789 – 1790Cleavage; by NIa-proBy similarity2
Sitei1842 – 1843Cleavage; by NIa-proBy similarity2
Sitei2031 – 2032Cleavage; by NIa-proBy similarity2
Sitei2274 – 2275Cleavage; by NIa-proBy similarity2
Sitei2790 – 2791Cleavage; by NIa-proBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Structurei

3D structure databases

ProteinModelPortaliQ85197.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini633 – 755Peptidase C6PROSITE-ProRule annotationAdd BLAST123
Domaini1226 – 1378Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST153
Domaini1397 – 1556Helicase C-terminalPROSITE-ProRule annotationAdd BLAST160
Domaini2032 – 2250Peptidase C4PROSITE-ProRule annotationAdd BLAST219
Domaini2516 – 2640RdRp catalyticPROSITE-ProRule annotationAdd BLAST125

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi349 – 352Involved in interaction with stylet and aphid transmissionBy similarity4
Motifi607 – 609Involved in virions binding and aphid transmissionBy similarity3
Motifi1328 – 1331DEFH box4
Motifi1883 – 1890Nuclear localization signalSequence analysis8

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 peptidase S30 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
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]
PfamiPF00270. 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: Q85197-1) [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
MATQVIMVGE FKILEVNCKP HAPVAAIHVP TQTPKTNDIK WADLEFTLAK
60 70 80 90 100
SLQRQAHGVV KVDKHGTARI KRASKHHMSC LEQQMADEVA EKEAFMAAPT
110 120 130 140 150
QLVTSIIFAG TTPPSMMETE TIVKKIHTVG KRAKVMRKRS YITPPTDKSL
160 170 180 190 200
RNHGVTPYSV QQLCRTLGNL SKRTGISLEV VGKTSKATKL RFTKTSFGHM
210 220 230 240 250
ARVQLKHHDG RMHRRDLVVD TSTTTIMQTL FLKTARTNAN LDVLTHGSSG
260 270 280 290 300
LVFWNYLVTG QRMRTRDNFI IVRGRCNGIL VDARAKLSES TMLSTHHYST
310 320 330 340 350
GDVFWRGFNR TFLENKPINL DHVCSSDFSV EECGSIAALI CQSLLPCGKI
360 370 380 390 400
TCRACAAKNL NMDEDTFKEF QTQRAREISA VIISEHPNFA CVSQFIDRYF
410 420 430 440 450
SHQRVLNPNV NAYREILKIV GGFTQSPYTH IQELNEILVL GGRATPEQLG
460 470 480 490 500
SASAHLLEIT RFVRNRTDNI KKGSLALFRN KISAKAHVNT ALMCDNQLDR
510 520 530 540 550
NGNLIWGERG YHAKRFFSNY FDIITPGGGY KQYIERRVPN GIRKLAIGNL
560 570 580 590 600
IVTTNLEALR EQLEGESIEK KAVTKACVSM SDNNYKYPCC CVTLDDGTPL
610 620 630 640 650
YSTFIMPTKN HLVIGNSGDP KFLDLPADIS TQMYIAKSGY CYINIFLAML
660 670 680 690 700
VNVDESDAKD FTKKVRDIIV PDLGEWPTLI DVATSCSLLS AFYPATSAAE
710 720 730 740 750
LPRILVDHDL KTMHVIDSYG SLNTGYHVLK ANTIRQLIQF ASNSLDSEMK
760 770 780 790 800
HYRVGGTSNS QINGYATIKM LAKAVYRPKL MKEIIHEQPF MLVMSLMSPG
810 820 830 840 850
ILIALANSGA LEMGIHHWIR EGDSLVKMAH MLRTVAQNVS VARATWVQQE
860 870 880 890 900
IISDSAQQML ETILNGTIPN VSYFQAIQYL TMLAASKEVD AEVRVTGYYT
910 920 930 940 950
FKLQTSELLE KTYLSLLEDS WQELSYFGRF QAIRHSRRYC TAGTIVVKPE
960 970 980 990 1000
RHVDLGGIYA TSYQFALAKQ MEYSKKAVCQ AVNGLQARFN NITSQIYCKI
1010 1020 1030 1040 1050
LNWPKRLFPD LVKFINTMLA ITVALQLYIA FATILRHHQQ CKQDSLELEY
1060 1070 1080 1090 1100
CKKERQLITL YDFFIAKQPY ATEEEFMAHV DEQNPDLSNF AREYCAEVVL
1110 1120 1130 1140 1150
FQAKASEQVN FERIIAFISL VLMMFDRERS DCVYRSLTKL KSLMSTVENT
1160 1170 1180 1190 1200
VQFQSLDDIG PTLEEKNMTI DFDLDTDTIV GKSIIGHTFK EWWDVQLNTN
1210 1220 1230 1240 1250
RIVPHYRTEG HFMEFTRANA PTIAHQIAHD LHTDIMLRGA VGSGKSTGLP
1260 1270 1280 1290 1300
YHLSKKGTVL LLEPTRPLAE NVTKQLKSDP FHVSPTLRMR GMAVFGSTPI
1310 1320 1330 1340 1350
HVMTTGFALH YLANNLKMLS TYDFIIIDEF HVHDSNAIAL RNLLHEHNYQ
1360 1370 1380 1390 1400
GKLIKVSATP PGREVEFSTQ YPVEIRVEDQ VSFQDFVKAQ GNGSNLDLTS
1410 1420 1430 1440 1450
KCDNLLVYVA SYNEVDQLSK LLLERHFLVT KVDGRSMKLG QVEIITKGSA
1460 1470 1480 1490 1500
NKKHFIVATN IIENGVTLDI DAVIDFGMKV VPFLDSDNRM ISYNKVSISY
1510 1520 1530 1540 1550
GERIQRLGRV GRNKAGVALR IGHTEKGISD VPVVIATQAA FLGFVYGLPI
1560 1570 1580 1590 1600
STQSVTTQVL SNVTLKQART MVQFELPIFY MAHLVRYDGT MHPAIHNELK
1610 1620 1630 1640 1650
KYKLRDSEIQ LRKLAIPSKC VPIWMTGKAY RLLTHNSQIP DDVRVPFLTK
1660 1670 1680 1690 1700
EIPDKLHENV WAIVEKFKCD AGIGRMTSAQ ASKVAYTLET DIHSVQRTIL
1710 1720 1730 1740 1750
IIDQLLEREM QKQSHFEMVT NQSCSSGMLS LQTMMNAIQS RYAKNHTAGN
1760 1770 1780 1790 1800
IEILQRAKAQ LLEFSNLSGD ISTESALREF GYLEAVQFQS GTQVSNFLGL
1810 1820 1830 1840 1850
EGHWKKSLIT KDLLIVGGVC VGAAWMIGEY FFKKSKGVVA FQGIISDRGK
1860 1870 1880 1890 1900
KLKFARARDE KMGHYVEAPD STLEHYFGSA YTKKGKTKGK THGMGKKNHR
1910 1920 1930 1940 1950
FVNMYGFDPS DYTFIRYVDP LTGYTLDESP YTDIRLIQSQ FSDIREQQLL
1960 1970 1980 1990 2000
NDELERNMVH YKPGVQGYLV KDKTSQILKI DLTPHIPLKV CDATNNIAGH
2010 2020 2030 2040 2050
PDREGELRQT GKGQLLDYAE LPQKKESVEF ESTSMFRGVR DYNPISSVIC
2060 2070 2080 2090 2100
QLENESEGRT TQLFGLGFGP FIITNQHLFV RNNGSLTVRS QMGVFKVNST
2110 2120 2130 2140 2150
VALQMRPVEG RDVLIIKMPK DFPPFPQRLK FRQPTHSEKV CLILTNFQQK
2160 2170 2180 2190 2200
SSSSMVSETS ILYQRKNTYF WKHWISTKEG HCGSPIVSTT DGAILGIHSL
2210 2220 2230 2240 2250
SNMTNTSNYF ACFPKGFTET YLATESVHEW VKGWKFNANN VCWGSFHLQD
2260 2270 2280 2290 2300
SKPTKEFKTV KLVTDLLGEA VYTQGCDSKW LFNAAHTNIQ AVAQLESNLV
2310 2320 2330 2340 2350
TKHTVKGKCK LFETYLNVDK AAHDFFSKYM GFYKPSKLNR EAYTQDLMKY
2360 2370 2380 2390 2400
SKVIQVGEVD CGVFESALTG LLHNLGRWGF TTACYTTDED SIYTALNMKA
2410 2420 2430 2440 2450
AVGALYRGKK RDYFDAMSPS EREHLLFLSC KRLYFGQLGV WNGSLKAELR
2460 2470 2480 2490 2500
PKEKVDLNKT RTFTAAPIET LLGGKVCVDD FNNMFYSLHL KAPWSVGMTK
2510 2520 2530 2540 2550
FYGTWNQLMC KLPDDWVYCD ADGSQFDSSI SPYMINAVLR IRLHFMEDWD
2560 2570 2580 2590 2600
IGSQMLQNLY TEIGTHQSQH QMAQLLKKFK GNNSGQPSTV VDNTLLVVLA
2610 2620 2630 2640 2650
LHYALLKSGI PLEEQDSVCA YGVNGDDLLI AIRPDMEHKL DGFQALFSEL
2660 2670 2680 2690 2700
GLNYEFNSRS KDKKDLWFMS HKAIQCGEIL IPKLEEERIV SILEWDRSHE
2710 2720 2730 2740 2750
PIHRLEAICA SMVESWGYPE LTHEIRRFYA WVLEQSPYNA LATTGLAPYI
2760 2770 2780 2790 2800
AESALKTLYT NVHPTSTELE KYSIQFDEQM DEEDDMVYFQ AETLDASEAL
2810 2820 2830 2840 2850
AQKSEGRKKE RESNSSKAVA VKDKDVDLGT AGTHSVPRLK SMTSKLTLPM
2860 2870 2880 2890 2900
LKGKSVVNLD HLLSYKPKQV DLSNARATHE QFQNWYDGVM ASYELEESSM
2910 2920 2930 2940 2950
EIILNGFMVW CIENGTSPDI NGVWTMMDNE EQVSYPLKPM LDHAKPSLRQ
2960 2970 2980 2990 3000
IMRHFSALAE AYIEMRSREK PYMPRYGLQR NLRDQSLARY AFDFYEITAT
3010 3020 3030 3040 3050
TPIRAKEAHL QMKAAALKNS NTNMFGLDGN VTTSEEDTER HTATDVNRNM

HHLLGVKGV
Note: Produced by conventional translation.
Length:3,059
Mass (Da):346,080
Last modified:November 1, 1996 - v1
Checksum:iEFE897679595693A
GO
Isoform P3N-PIPO polyprotein (identifier: P0CK05-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0CK05.
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:993
Mass (Da):111,268
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21670 Genomic RNA. Translation: CAA79766.1.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21670 Genomic RNA. Translation: CAA79766.1.

3D structure databases

ProteinModelPortaliQ85197.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC04.014.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
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]
PfamiPF00270. 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_PVMA
AccessioniPrimary (citable) accession number: Q85197
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: November 1, 1996
Last modified: October 5, 2016
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

6K1 and 6K2 are involved in infectivity, as their deletion renders PVA non-infectious.

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.