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Protein

Genome polyprotein

Gene
N/A
Organism
Soybean mosaic virus (strain G2) (SMV)
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.
Both 6K peptides are indispensable for virus replication.By similarity
Nuclear inclusion protein A: has RNA-binding and proteolytic activities.

Catalytic activityi

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.
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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei262For P1 proteinase activityBy similarity1
Active sitei651For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei724For helper component proteinase activityPROSITE-ProRule annotation1
Active sitei2087For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2122For nuclear inclusion protein A activityPROSITE-ProRule annotation1
Active sitei2192For nuclear inclusion protein A activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1249 – 1256ATPPROSITE-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

MEROPSiC06.001.

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
OrganismiSoybean mosaic virus (strain G2) (SMV)
Taxonomic identifieri103931 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stagePotyviridaePotyvirus
Virus hostiGlycine max (Soybean) (Glycine hispida) [TaxID: 3847]
Proteomesi
  • UP000007189 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_00004200221 – 3066Genome polyproteinAdd BLAST3066
ChainiPRO_00000404281 – 308P1 proteinaseSequence analysisAdd BLAST308
ChainiPRO_0000040429309 – 765Helper component proteinaseSequence analysisAdd BLAST457
ChainiPRO_0000040430766 – 1112Protein P3By similarityAdd BLAST347
ChainiPRO_00000404311113 – 11646 kDa protein 1By similarityAdd BLAST52
ChainiPRO_00000404321165 – 1798Cytoplasmic inclusion proteinBy similarityAdd BLAST634
ChainiPRO_00000404331799 – 18516 kDa protein 2By similarityAdd BLAST53
ChainiPRO_00000404341852 – 2041Viral genome-linked proteinBy similarityAdd BLAST190
ChainiPRO_00000404352042 – 2284Nuclear inclusion protein ABy similarityAdd BLAST243
ChainiPRO_00000404362285 – 2801Nuclear inclusion protein BBy similarityAdd BLAST517
ChainiPRO_00000404372802 – 3066Capsid proteinBy similarityAdd BLAST265

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1915O-(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
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
Sitei308 – 309Cleavage; by P1 proteinaseSequence analysis2
Sitei765 – 766Cleavage; by autolysisPROSITE-ProRule annotation2
Sitei1112 – 1113Cleavage; by NIa-proBy similarity2
Sitei1164 – 1165Cleavage; by NIa-proBy similarity2
Sitei1798 – 1799Cleavage; by NIa-proBy similarity2
Sitei1851 – 1852Cleavage; by NIa-proBy similarity2
Sitei2041 – 2042Cleavage; by NIa-proBy similarity2
Sitei2284 – 2285Cleavage; by NIa-proBy similarity2
Sitei2801 – 2802Cleavage; by NIa-proBy similarity2

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Structurei

3D structure databases

ProteinModelPortaliQ90069.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini643 – 765Peptidase C6PROSITE-ProRule annotationAdd BLAST123
Domaini1236 – 1388Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST153
Domaini1407 – 1566Helicase C-terminalPROSITE-ProRule annotationAdd BLAST160
Domaini2042 – 2260Peptidase C4PROSITE-ProRule annotationAdd BLAST219
Domaini2526 – 2650RdRp catalyticPROSITE-ProRule annotationAdd BLAST125

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi361 – 364Involved in interaction with stylet and aphid transmissionBy similarity4
Motifi617 – 619Involved in virions binding and aphid transmissionBy similarity3
Motifi1338 – 1341DECH box4
Motifi1891 – 1900Nuclear localization signalSequence analysis10

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: Q90069-1) [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
MATIMIGSMA ISVPNTHVSR ASNSVMPVQA VQMAKQVPSA RGVLYTLKRE
60 70 80 90 100
GSTQVIKHEE ALRKFQEAFD QDVGIQRRLL VNKHSSIQST KEGWFDLASL
110 120 130 140 150
NFRAGSSKEA AIARRKQEEE DFLNGKYEQQ FYAGVSATKS MKFEGGSVGF
160 170 180 190 200
RTKYWRPTPK KTKERRATSQ CRKPTYVLEE VLSIASKSGK LVEFITGKGK
210 220 230 240 250
RVKVCYVRKH GAILPKFSLP HEEGKYIHQE LQYASTYEFL PYICMFAKYK
260 270 280 290 300
SINADDITYG DSGLLFDERS SLTTNHTKLP YFVVRGRRNG KLVNALEVVE
310 320 330 340 350
NMEDIQHYSQ NPEAQFFRGW KKVFDKMPPH VENHECTIDF TNEQCGELAA
360 370 380 390 400
AISQSIFPVK KLSCKQCRQH IKHLSWEEYK QFLLAHMGCH GAEWETFQEI
410 420 430 440 450
DGMRYVKRVI ETSTAENASL QTSLEIVRLT QNYKSTHMLQ IQDINKALMK
460 470 480 490 500
GPSVTQSELE QASKQLLAMT QWWKNHMALT DEDALKVFRN KRSSKALLNP
510 520 530 540 550
SLLCDNQLDK NGNFVWGERG RHSKRFFANY FEEVVPSEGY SKYVIRTNPN
560 570 580 590 600
GQRELAIGSL IVPLDFERAR MALQGKSVTR EPITMSCISR QDGNFVYPCC
610 620 630 640 650
CVTHDDGKAF YSELKSPTKR HLVIGTSGDP KYIDLPATDA DRMYIAKEGF
660 670 680 690 700
CYLNIFLAML VNVNEDEAKD FTKMVRDVIV PRLGKWPTML DVATAAYMLT
710 720 730 740 750
VFHPETRNAE LPRILVDHAC QTMHVIDSFG SLTVGYHVLK AGTVNQLIQF
760 770 780 790 800
ASNDLQSEMK FYRVGGEVQQ RMKCETALIT SIFKPKRMIQ ILENDPYILL
810 820 830 840 850
MGLVSPSILI HMYRMKHFEK GVELWISKEH SVAKIFIILG QLTKRVAAND
860 870 880 890 900
VLLEQLEMIS ETSERFMSIL EDCPQAPHSY KTAKDLLTMY IEGKASNNQL
910 920 930 940 950
VENGFVDMND KLYMAYEKIY SDRLKQEWRA LSWLEKFSIT WQLKRFAPHT
960 970 980 990 1000
EKCLTKKVVE ESSASSGNFA SVCFMNAQSH LRNVRNTLFQ KCDQVWTASV
1010 1020 1030 1040 1050
RAFVRLIIST LHRCYSDIVY LVNICIIFSL LVQMTSVLQG IVNTARRDKA
1060 1070 1080 1090 1100
LLSGWKRKED EEAVIHLYEM CEKMEGGHPS IEKFLDHVKG VRPDLLPVAV
1110 1120 1130 1140 1150
SMTGQSEDVS AQAKTATQLQ LEKIVAFMAL LTMCIDNERS DAVFKVLSKL
1160 1170 1180 1190 1200
KAFFSTMGED VKVQSLDEIQ SIDEDKKLTI DFDLETNKES SSVSFDVKFE
1210 1220 1230 1240 1250
AWWNRQLEQN RVIPHYRSTG EFLEFTRETA AKIANLVATS SHTEFLIRGA
1260 1270 1280 1290 1300
VGSGKSTGLP HHLSRKGKVL LLEPTRPLAE NVSKQLSFEP FYHNVTLRMR
1310 1320 1330 1340 1350
GLSKFGSSNI VVMTSGFAFH YYFNNPQQLS DFDFIIIDEC HVQDSPTIAF
1360 1370 1380 1390 1400
NCALKEFEFS GKLIKVSATT PGRECEFTTQ HPVKLKVEDH LSFQNFVQAQ
1410 1420 1430 1440 1450
GTGSNADMIQ HGNNLLVYVA SYNEVDQLSR LLTEKHYKVT KVDGRTMQMG
1460 1470 1480 1490 1500
NVEIATTGTE VKPHFIVATN IIENGVTLDI DCVIDFGLKV VATLDTDNRC
1510 1520 1530 1540 1550
VRYNKQSVSY GERIQRLGRV GRCKPGFALR IGHTGKGVEE VPEFIATEAA
1560 1570 1580 1590 1600
FLSFAYGLPV TTQSVSTNIL SRCTVKQARV ALNFELTPFF TTNFIKYDGS
1610 1620 1630 1640 1650
MHVIDTRLLK SYKLRESEML LTKLAIPYQF VGQWVTVKEY ERQGIHLNCP
1660 1670 1680 1690 1700
EKVKIPFYVH GIPDKLYEML WDTVCKYKND AGFGSVKSVN ATKISYTLST
1710 1720 1730 1740 1750
DPTAIPRTLA ILDHLLSEEM TKKSHFDTIG SAVTGYSFSL AGIADGFRKR
1760 1770 1780 1790 1800
YLKDYTQHNI AVLQQAKAQL LEFDCNKVDI NNLHNVEGIG ILNAVQLQSK
1810 1820 1830 1840 1850
HEVSKFLQLK GKWDGKKFMN DAVVAIFTLV GGGWMLWDYF TRVIREPVST
1860 1870 1880 1890 1900
QGKKRQIQKL KFRDAFDRKI GREVYADDYT MEHRFGEAYT KKGKQKGSTR
1910 1920 1930 1940 1950
TKGMGRKSRN FIHLYGVEPE NYSMIRFVDP LTGHTMDEHP RVDIRMVQQE
1960 1970 1980 1990 2000
FEEIRKDMIG EGELDRQRVY HNPGLQAYFI GKNTEEALKV DLTPHRPTLL
2010 2020 2030 2040 2050
CQNSNAIAGF PEREDELRQT GLPQVVSKSD VPRAKERVEM ESKSVYKGLR
2060 2070 2080 2090 2100
DYSGISTLIC QLTNSSDGHK ETMFGVGYGS FIITNGHLFR RNNGMLTVKT
2110 2120 2130 2140 2150
WHGEFVIHNT TQLKIHFIQG RDVILIRMPK DFPPFGKRNL FRQPKREERV
2160 2170 2180 2190 2200
CMVGTNFQEK SLRATVSESS MILPEGKGSF WIHWITTQDG FCGLPLVSVN
2210 2220 2230 2240 2250
DGHIVGIHGL TSNDSEKNFF VPLTDGFEKE YLENADNLSW DKHWFWEPSK
2260 2270 2280 2290 2300
IAWGSLNLVE EQPKEEFKIS KLVSDLFGNT VTVQGRKERW VLDAMEGNLA
2310 2320 2330 2340 2350
ACGQDDSALV TKHVVKGKCP YFAQYLSVNQ EAKSFFEPLM GAYQPSRLNK
2360 2370 2380 2390 2400
DAFKRGFFKY NKPVVLNEVD FQSFERAVAG VKLMMMEFDF KECVYVTDPD
2410 2420 2430 2440 2450
EIYDSLNMKA AVGAQYKGKK QDYFSGMDSF DKERLLYLSC ERLFYGEKGV
2460 2470 2480 2490 2500
WNGSLKAELR PIEKVQANKT RTFTAAPIDT LLGAKVCVDD FNNQFYSLNL
2510 2520 2530 2540 2550
TCPWTVGMTK FYRGWDKLMR SLPDGWVYCH ADGSQFDSSL TPLLLNAVLD
2560 2570 2580 2590 2600
VRSFFMEDWW VGREMLENLY AEIVYTPILA PDGTIFKKFR GNNSGQPSTV
2610 2620 2630 2640 2650
VDNTLMVVIA LYYSGCKQGW SEEDIQERLV FFANGDDIIL AVSDKDTWLY
2660 2670 2680 2690 2700
DTLSTSFAEL GLNYNFEERT KKREELWFMS HKAMLVDGIY IPKLEPERIV
2710 2720 2730 2740 2750
SILEWDRSKE LMHRTEAICA SMIEAWGYTE LLQEIRKFYL WLLNKDEFKE
2760 2770 2780 2790 2800
LASSGKAPYI AETALRKLYT DVNAQTSELQ RYLEVLDFTH ADDCCESVSL
2810 2820 2830 2840 2850
QSGKEKEGDM DAGKDPKKST SSSKGAGTSS KDVNVGSKGK VVPRLQKITR
2860 2870 2880 2890 2900
KMNLPMVEGK IILSLDHLLE YKPNQVDLFN TRATRTQFEA WYNAVKDEYE
2910 2920 2930 2940 2950
LDDEQMGVVM NGFMVWCIDN GTSPDANGVW VMMDGEEQIE YPLKPIVENA
2960 2970 2980 2990 3000
KPTLRQIMHH FSDAAEAYIE MRNSESPYMP RYGLLRNLRD RELARYAFDF
3010 3020 3030 3040 3050
YEVTSKTPNR AREAIAQMKA AALSGVNNKL FGLDGNISTN SENTERHTAR
3060
DVNQNMHTLL GMGPPQ
Note: Produced by conventional translation.
Length:3,066
Mass (Da):349,543
Last modified:November 1, 1996 - v1
Checksum:i2188A79DBD155399
GO
Isoform P3N-PIPO polyprotein (identifier: P0CK07-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0CK07.
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:992
Mass (Da):113,575
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S42280 Genomic RNA. Translation: AAB22819.2.
PIRiJQ1661.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S42280 Genomic RNA. Translation: AAB22819.2.
PIRiJQ1661.

3D structure databases

ProteinModelPortaliQ90069.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC06.001.

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_SBMVG
AccessioniPrimary (citable) accession number: Q90069
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 122 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.