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Protein

Genome polyprotein

Gene
N/A
Organism
Ryegrass mosaic virus (isolate Denmark/Danish) (RGMV)
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.By similarity
Nuclear inclusion protein B: an RNA-dependent RNA polymerase that plays an essential role in the virus replication.By similarity
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.By similarity

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 sitei173For P1 proteinase activityBy similarity1
Active sitei182For P1 proteinase activitySequence analysis1
Active sitei215For P1 proteinase activityBy similarity1
Active sitei598For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei670For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei2045For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2080For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2149For nuclear inclusion protein A activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1202 – 1209ATPPROSITE-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

MEROPSiC04.012.

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
OrganismiRyegrass mosaic virus (isolate Denmark/Danish) (RGMV)
Taxonomic identifieri652106 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stagePotyviridaeRymovirus
Virus hostiDactylis glomerata (Orchard grass) (Cock's-foot grass) [TaxID: 4509]
Lolium [TaxID: 4520]
Proteomesi
  • UP000000568 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_00004200211 – 3086Genome polyproteinAdd BLAST3086
ChainiPRO_50001469921 – 256P1 proteinaseSequence analysisAdd BLAST256
ChainiPRO_5000146993257 – 711Helper component proteinaseSequence analysisAdd BLAST455
ChainiPRO_5000146994712 – 1063Protein P3Sequence analysisAdd BLAST352
ChainiPRO_50001469951064 – 11166 kDa protein 1Sequence analysisAdd BLAST53
ChainiPRO_50001469961117 – 1753Cytoplasmic inclusion proteinSequence analysisAdd BLAST637
ChainiPRO_50001469971754 – 18066 kDa protein 2Sequence analysisAdd BLAST53
ChainiPRO_50001469981807 – 1999Viral genome-linked proteinSequence analysisAdd BLAST193
ChainiPRO_50001469992000 – 2240Nuclear inclusion protein ASequence analysisAdd BLAST241
ChainiPRO_50001470002241 – 2758Nuclear inclusion protein BSequence analysisAdd BLAST518
ChainiPRO_50001470012759 – 3086Capsid proteinSequence analysisAdd BLAST328

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1870O-(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 (By similarity).By similarity
Genome polyprotein of potyviruses 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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei256 – 257Cleavage; by P1 proteinaseSequence analysis2
Sitei711 – 712Cleavage; by autolysisPROSITE-ProRule annotation2
Sitei1063 – 1064Cleavage; by NIa-proBy similarity2
Sitei1116 – 1117Cleavage; by NIa-proBy similarity2
Sitei1753 – 1754Cleavage; by NIa-proBy similarity2
Sitei1806 – 1807Cleavage; by NIa-proBy similarity2
Sitei1999 – 2000Cleavage; by NIa-proBy similarity2
Sitei2240 – 2241Cleavage; by NIa-proBy similarity2
Sitei2758 – 2759Cleavage; by NIa-proBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Structurei

3D structure databases

ProteinModelPortaliO11436.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini590 – 711Peptidase C6PROSITE-ProRule annotationAdd BLAST122
Domaini1189 – 1341Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST153
Domaini2000 – 2217Peptidase C4PROSITE-ProRule annotationAdd BLAST218
Domaini2482 – 2606RdRp catalyticPROSITE-ProRule annotationAdd BLAST125

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1291 – 1294DEAH box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi2769 – 2821Thr-richAdd BLAST53

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 (By similarity).By similarity

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.
InterProiIPR001456. 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]
PfamiPF00271. 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]

Sequencei

Sequence statusi: Complete.

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

O11436-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMNFGSLNVG LKQVDGTWVP RVFEEKEMAR LLAEKQHARV MRATQEMMKA
60 70 80 90 100
PNPFAEFDEM HQRGNPFAGR VRKCETREPK SAQKPIVTVD TVPVAIYTDV
110 120 130 140 150
IWPENGKVHA LSRRRAPRKH ARRSKILACD LLTQVLNISR RAGKSVEVIG
160 170 180 190 200
KRRCCLKPRR RDGKSCFGVI TKHHKGVLSS RDMVKDLFVD SIIEHIAYTG
210 220 230 240 250
HTPLIDAADI KPGDSGLIYR EKKDGYVTRV VRGRHDGDII DARDYVRAGI
260 270 280 290 300
HTIKHYSDDG KSLVKYAPYC QPSHHTFGHM CRVTWSDTEI LQFREMLSQA
310 320 330 340 350
IMPQRDPRCD ICAEVAGQRT KDEILQHART SQMMQMLEFG KEDERWKAPR
360 370 380 390 400
RVMETLLEES NWPSMDYSTS SEITTICCGN NDEPFRRIYS IMKVLAEPNL
410 420 430 440 450
ADVSAWQEAN SSLLQLARYM KNREMSVQAG NSATFTNPFP PTVHTFGPTN
460 470 480 490 500
NGADILQGPW DNWGDKQPIA LAFFEKHFNK WQINEFSIDR RVRKHIRGTR
510 520 530 540 550
KLALMDLNQS RSIKDLEDHV QEEEIPYERK TESCITMYKD QYLYSCSCVT
560 570 580 590 600
ARDGKPYLSM RYLQATGLIP IARGADVQHM PNSDSWQGFY YVAPEGYCYI
610 620 630 640 650
NIFLPMLALA PYYKVGKLSE LIGKLIKVLG KWPKLKDVAL ACLYITEYHT
660 670 680 690 700
YAQNALLPPI LVHHSTRTMH VVDTLGSLSV GYHVLKAGTV KHLVNLASRL
710 720 730 740 750
ATGEMLDYNV GGSLGGIHAY DLLIRSTFDH VLLERALETD PYYILYSALS
760 770 780 790 800
PTVLKQMYTS KSYANALRVF VRSNQSLFQV VCTLENLARR MTRAQSIEQQ
810 820 830 840 850
IMQLQSLYPQ LLDMLADNIP DSPLSWLSHH VTTDSMQRAI ELNNCDIELA
860 870 880 890 900
RGGYASINTS WRKKKEQYYA DLIKEYYNAL SPQAKIFVSR AYIGYLHATT
910 920 930 940 950
PLFANARKIS SEIASNICTQ AYSRTIGRGI SIVSSGGRKG KTWLTARGDS
960 970 980 990 1000
FYKTMISRAI KLYTPEVSAV IGVATVVGIL LSTMTTLHTY LVKNKQTAQK
1010 1020 1030 1040 1050
TNEKFEELMY DKVALYIPKY DAEHSHLQGK DLDFEHFARW LMARDKKLSS
1060 1070 1080 1090 1100
FVQSHLVDTV THQAKDDTNV WIEKCIATIV LMMMAIDSNK SDKLYQILCK
1110 1120 1130 1140 1150
LRTVFSTMGQ TVVTHQSIDE ILDIDESKRT TIDFERVEVM QPTQPILKTT
1160 1170 1180 1190 1200
FEGFWDMQIQ MGRTVAHYRT TGRLVELTRE NIAEVVATIS SDTANAEFIV
1210 1220 1230 1240 1250
RGGVGTGKST SLPTALCERG RVLMLEPTRP LTENVAQQLR GEPHFKSPSV
1260 1270 1280 1290 1300
HMRGLNTFGS SRITIMTSGY ALHYYANNRQ LLRDFEFIMF DECHVMDSSA
1310 1320 1330 1340 1350
MAFYSLCNDA KVAAKLLKVS ATPAGRECEF KPMFPVRVSE AAQLSFESFV
1360 1370 1380 1390 1400
TAQGSKSTYD IIQYGNNILV YVASYNEVDK LAAMLLEKRF RVTKVDGRTM
1410 1420 1430 1440 1450
KLNTHGIELH GTAQVKHFIV ATNIIENGVT LEIDCLVDFG TKVVAQLDTE
1460 1470 1480 1490 1500
GRRIMYMKVP ISYGERIQRL GRVGRTKPGA RLKVGHTMRG IVEIPEVIAT
1510 1520 1530 1540 1550
EAAFQCFMYD LPVMTGQVSV SLLSKCTREQ ARTMAAFELS PFTMSNLVAF
1560 1570 1580 1590 1600
DGTMHPAIHD LLKKFKLRDS TVVLRRTALP LRASASWYTV REYETIIGDL
1610 1620 1630 1640 1650
HIENKDVRIP FVANDLSNSL LEGLWDAIQC NRSDVSTTKL TTVSANKIAY
1660 1670 1680 1690 1700
TLKTDTSSIQ RTISIIDDLL AEERKKQEMF THHLSTTSGG YTFGLNAIAM
1710 1720 1730 1740 1750
CIKSRYAKGY CIENIATLTN VRNQLTEFSG MSEDQYTSEI IQNYPDLTLV
1760 1770 1780 1790 1800
HHQSKQEIIR NLKLKAKYDQ TLIASDLLLG TAVLIGGGAM LYKTFMTETN
1810 1820 1830 1840 1850
TRVHLEGDGK RQREKLQYRA ARDSKQDYEV YADEREIQEN YGEAYTKHGR
1860 1870 1880 1890 1900
KGPAHEKGTG SKTREFTNFY GFDPAEYDTV RLVDPITGKT CDKAVRDLLR
1910 1920 1930 1940 1950
MRDVADTFAE IRESMDEDMI LQPGVNFAPA LIEAYFMNSR TNAARRVDLV
1960 1970 1980 1990 2000
PHNPMQVGRL SNNIAGFPTH DGELRQSRPS RPIQKDQVPA ANEYSVQHES
2010 2020 2030 2040 2050
KSIAKGLRDY HPVSSNLCAL EYYCGDMRTS IYGVCYGPYI LTTAHLIKEK
2060 2070 2080 2090 2100
GGWLKIRTKH GLFKLEAMDR VQIRELCGSD IIVIKGPKDM PPAPMRLKFR
2110 2120 2130 2140 2150
APKSGERAVL VGFVDDNLDR QLVSDSSAVY RRENTGFWKH WITTKYGNCG
2160 2170 2180 2190 2200
LPMVSVDTMD IIGLHSLGAQ NSNENYFAAL TDDFSKQFFE PETDVPWQRK
2210 2220 2230 2240 2250
WSYNADKVNY GTMDLTSNQP SGAFKTTKLL EDLLEAVSHQ SQEYTWLTKY
2260 2270 2280 2290 2300
CGANLLVIGK CPGNLITKHV IKGKSPTFDL FLSVDAQASD FFKPLMGDYA
2310 2320 2330 2340 2350
PSRLNREAFV KDITKYDTEI PIGNLSITDF ENAVEDTYYI LKDSGIEQCN
2360 2370 2380 2390 2400
YITDAIPIFD SMNMKAATGA LYGGKKKDYF ENYTDDMKQN ILKESYIRLR
2410 2420 2430 2440 2450
EGKMGIWNGS LKAELRSKEK VEANKTRVFT AAPLDTLLAG KGCVDDFNNQ
2460 2470 2480 2490 2500
FYAAHLKGPW TVGITKFFGR WNDFLSELPP GWDYFDADGS RFDSSLTPFL
2510 2520 2530 2540 2550
LNAVLNIRKK FMINWAFGQR CLGNLYTEII YTPIATPDGS VVKKMRGNNS
2560 2570 2580 2590 2600
GQPSTVVDNT IMVIIAMQYA ISKAEFPAGR LRDQIRYFAN GDDLVVAVEP
2610 2620 2630 2640 2650
SLSDKISSFS ASFAELGLSY DFSNKVNDRS ELQFMSHTGK LIDGMYIPML
2660 2670 2680 2690 2700
ERERICAILE WSRSDEPQFQ LDAISAAMIE AWGDDELLYQ IRRYYSWLLE
2710 2720 2730 2740 2750
QEPYKSIAEL GHAPYLAEAA LKALYTGKDP DAELIAIYER AMLNTPPTED
2760 2770 2780 2790 2800
RPTKVVHEAN VTAASSAATQ TSTTSPTVTS TSGASTSTSS GTTSAPLAST
2810 2820 2830 2840 2850
TPPVSATTTP STGTTAPTTP TVRAANLPDI AGHRKAKANG ESQLNVRGEN
2860 2870 2880 2890 2900
DDEDVPAASE FALPRLPTLG AKIRVPKFKG AIVLNKDHLI KYTPDQRDLS
2910 2920 2930 2940 2950
NTRATQEQFE KWYSGVRNEV EKTDEEMALL LNGSMVWCME NGTSPDLSGS
2960 2970 2980 2990 3000
WTMMEGEEQI AYPLEPFCRH AQPTLRSIMA HFSDAATAYV VLRNQKSRYM
3010 3020 3030 3040 3050
PRYGLKRGLN DYSLAPYAFD FYEITSTSPL RARERHAQMK AAAIRGKASR
3060 3070 3080
MFGLDGNVSA QSENTERHTV EDVNTRVHSL SGANML
Length:3,086
Mass (Da):347,695
Last modified:July 1, 1997 - v1
Checksum:i662EB273DD2CAE72
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y09854 Genomic RNA. Translation: CAA70983.1.
RefSeqiNP_044727.1. NC_001814.1.

Genome annotation databases

GeneIDi1403650.
KEGGivg:1403650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y09854 Genomic RNA. Translation: CAA70983.1.
RefSeqiNP_044727.1. NC_001814.1.

3D structure databases

ProteinModelPortaliO11436.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC04.012.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1403650.
KEGGivg:1403650.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR001456. 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]
PfamiPF00271. 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_RGMVD
AccessioniPrimary (citable) accession number: O11436
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 30, 2010
Last sequence update: July 1, 1997
Last modified: September 16, 2015
This is version 107 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, Reference 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.