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Q6XW15

- POLG_BTMV

UniProt

Q6XW15 - POLG_BTMV

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Protein
Genome polyprotein
Gene
N/A
Organism
Beet mosaic virus (BtMV)
Status
Reviewed - 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.
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 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).
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
Sitei313 – 3142Cleavage; by P1 proteinase Reviewed prediction
Active sitei656 – 6561For helper component proteinase activity By similarity
Active sitei729 – 7291For helper component proteinase activity By similarity
Sitei770 – 7712Cleavage; by HC-pro Reviewed prediction
Sitei1117 – 11182Cleavage; by NIa-pro By similarity
Sitei1169 – 11702Cleavage; by NIa-pro By similarity
Sitei1803 – 18042Cleavage; by NIa-pro By similarity
Sitei1855 – 18562Cleavage; by NIa-pro By similarity
Sitei2046 – 20472Cleavage; by NIa-pro By similarity
Active sitei2092 – 20921For nuclear inclusion protein A activity By similarity
Active sitei2127 – 21271For nuclear inclusion protein A activity By similarity
Active sitei2198 – 21981For nuclear inclusion protein A activity By similarity
Sitei2293 – 22942Cleavage; by NIa-pro By similarity
Sitei2809 – 28102Cleavage; by NIa-pro By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1254 – 12618ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. RNA binding Source: InterPro
  3. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  4. cysteine-type endopeptidase activity Source: InterPro
  5. helicase activity Source: UniProtKB-KW
  6. structural molecule activity Source: InterPro

GO - Biological processi

  1. RNA-protein covalent cross-linking Source: UniProtKB-KW
  2. transcription, DNA-templated Source: InterPro
  3. viral RNA genome replication Source: InterPro
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

MEROPSiS30.001.

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
OrganismiBeet mosaic virus (BtMV)
Taxonomic identifieri114921 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stagePotyviridaePotyvirus
Virus hostiAmaranthus retroflexus (Redroot amaranth) (Redroot pigweed) [TaxID: 124763]
Beta vulgaris subsp. maritima (Sea beet) (Beta maritima) [TaxID: 350892]
Beta vulgaris subsp. vulgaris (sugar beet) [TaxID: 3555]
Chenopodium album (Lamb's-quarters) [TaxID: 3559]
Melilotus indicus (Sourclover) (Yellow sweet clover) [TaxID: 200951]
Sonchus arvensis (Perennial sowthistle) [TaxID: 50192]
Spinacia oleracea (Spinach) [TaxID: 3562]
Trifolium incarnatum (Crimson clover) [TaxID: 60916]
ProteomesiUP000007617: Genome

Subcellular locationi

Chain Capsid protein : Virion Reviewed prediction

GO - Cellular componenti

  1. helical viral capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Helical capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 30853085Genome polyprotein
PRO_0000419994Add
BLAST
Chaini1 – 313313P1 proteinase Reviewed prediction
PRO_0000040246Add
BLAST
Chaini314 – 770457Helper component proteinase Reviewed prediction
PRO_0000040247Add
BLAST
Chaini771 – 1117347Protein P3 Reviewed prediction
PRO_0000040248Add
BLAST
Chaini1118 – 1169526 kDa protein 1 By similarity
PRO_0000040249Add
BLAST
Chaini1170 – 1803634Cytoplasmic inclusion protein By similarity
PRO_0000040250Add
BLAST
Chaini1804 – 1855526 kDa protein 2 By similarity
PRO_0000040251Add
BLAST
Chaini1856 – 2046191Viral genome-linked protein By similarity
PRO_0000040252Add
BLAST
Chaini2047 – 2293247Nuclear inclusion protein A By similarity
PRO_0000040253Add
BLAST
Chaini2294 – 2809516Nuclear inclusion protein B By similarity
PRO_0000040254Add
BLAST
Chaini2810 – 3085276Capsid protein
PRO_0000040255Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1919 – 19191O-(5'-phospho-RNA)-tyrosine By 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.
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.

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Structurei

3D structure databases

ProteinModelPortaliQ6XW15.
SMRiQ6XW15. Positions 2055-2269.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1241 – 1393153Helicase ATP-binding
Add
BLAST
Domaini1412 – 1571160Helicase C-terminal
Add
BLAST
Domaini2047 – 2266220Peptidase C4
Add
BLAST
Domaini2535 – 2659125RdRp catalytic
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi365 – 3684Involved in interaction with stylet and aphid transmission By similarity
Motifi622 – 6243Involved in virions binding and aphid transmission By similarity
Motifi1343 – 13464DESH box
Motifi1895 – 190410Nuclear localization signal Reviewed prediction

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

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR001456. Peptidase_C6.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[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.
PROSITEiPS51192. 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. Align

Isoform Genome polyprotein (identifier: Q6XW15-1) [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.

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MATMMHFGQF PSNIPLRAAT CCTKVHSTLV TKEMMASSVK PAESSSVARP     50
IIYSSAATDG YEKAQRAFEA SFREKYSGKL EAMKYGKMVK KGGLTYVKRA 100
GPQAIAKGIE MDAAIEKFNT AFNAGELENV TLEGDITAGI SVARGESVWL 150
RSVFWSRSLK KQARKKTPKL VAKSDFDDLF NKVLKVASLG NIPVEIVGKK 200
ANKILRCGYR RVNTSTIPYF HLPHHNSNYI CRELHPQRVR WLVPLLVRHR 250
KIRDQFSDSM IARGWSGLIL PKYIASTCGR RYDEVIVRGR LYGRVEDART 300
KLPAGDVGRT MHYSSGEERF FAGWKEGFEK LVPAQKEHIC KIVQDNKFCG 350
KLAASIVQIA FPCHKMACDV CRNKFNEMTP EAYSELIDKH IDQRMNEINE 400
AIVRFPGLKQ VVSNFRSKHI ASTNIKDNLE VAKLTQGHKA NQMMQLARIN 450
SILIKGNTAT PSEISDASGL LLEITRWFNN HLSVIDKGSL RAFRNKRSSK 500
ALVNPSLLCD NQRDKNGNFI WGERGYHSKR FFASHFDEVT PGDGYKEYII 550
RKGPQGQRKL AIGNLIVSFD LEKTRQALKG EEVEKLPLSN SCVSKRNGNY 600
VYTSCCVTLD DGTPLYSNIK NPTKRHLVVG TTGDPKIVDL PATDTDKMYI 650
AKEGYCYLNI FLAMLINVNE NEAKAFTKMV RDIIIPMLGT WPTMQDLATA 700
CFMMTAFFPE TSSAELPRIL VDHTNQTMHV IDSFGSLTTG YHVLKAGTAA 750
QLIDFASTEL EGEMKWYRVG GHGLPVKEKM ISALITSIFR PKKLVYLIEE 800
DPYVLIMAMC SPRLIISLFN NGALELAAKH WISRDKNVSA IFAMLMDLST 850
EMSKAELLIE QHRMINECAK RVHDTQNYLD EVGPHQQEVR TFLALISDEL 900
EADKELHKTG FANFSERFHS LTEKMYVDAL EEEWRGLSLL DRFSYATFVY 950
KHKPRSTSVL PPKKSEDIDA KFVISPSWFV GKTKEHLSGG RKYVTSQITQ 1000
FTSYIKRATL DRAMRIMCSC LKDLAYFMNV ALVTHLLISM IAAVYNMLND 1050
HRIAKRRLYI LEMQETNTAI WHLYDTWKTV NQRDPTHEEF RKYVAKVNKN 1100
LLRHLPEEED KAEVEYQANK VYEKKLEKAV ALMALFTMIF DTEKSGAVFS 1150
ILRNIKSVFS TLGEEVKYQS LDEIQSIEDE KKLTIDFDLD TEITAEHTTM 1200
DVQFEKWWDK QLSQNRVVPH YRVGGTFIEF TRHTAASVCN TICASSEQEF 1250
VVRGAVGSGK STGLPSHLSR KGRVLLLEPT RPLAENVCKQ LRKEPFHLSP 1300
TLRMRGLTTF GSSNISVMTS GYALHFHANN PQRLEEFDFI MIDESHTMDS 1350
STMAFYCLLR EYEFKGKILK VSATPPGREC EFKTQHDVLI KIEESLSYNS 1400
FVTAQGTGSN ADVVQNGDNI LVYVPSYNDV DQLSKGLMEK GHLVTKVDGR 1450
TMKMGNVEIP TKGTSSKKHF IVATNIIENG VTLDIDVVVD FGLKVVAELD 1500
SDSRCMRYKK VSISYGERLQ RLGRVGRVKQ GTALRIGHTE TGMTEIPVAI 1550
ATEAAFICFA YNLPVMTHNV TSSLLSRCTN RQARTMMQYE LSPFFMVELV 1600
HFNGCVHPQI ESKLKAYKLR DSETQLSTLA IPNSGTSRWK TVGEYKKLGV 1650
RIEADDNVRV PFAANGVPDR LYADLWETIQ QHKSDAGFGR LTSACASKIS 1700
YTLTTQPNAI PRTLAIIEHL LREEQQKKAY FESLNDTLCA TSFSLAGMVN 1750
NIRRRYLKDH SAHNINVLQN AKSQLNEFNS KAIDPERVGD IMGYGVLDTV 1800
QYQSATDVQK RLKLKGRWNG SLAATDLLIA GAVFAGGCWM LWEYTKSGNE 1850
IVQYQGKRRQ MQKLKFRNAR DNKVGREVYG DDGTIEHFFG AAYTERGKRK 1900
GNNSTKGMGT KTRRFVHMYG FDPTEYSFVR FVDPLTGYSK DESVQTDISL 1950
VQSEIGEYRQ KCMEDDDELI DFIKQKPGIQ AYFMKNGSDK ALQVDLTPHI 2000
PLLSCAKTAT IAGFPERESE LRQTGTPIVV NKNVVPGEHK EVVREEGKSI 2050
VKGLRNYNPI SSVVCRLTND SNGNAQTLYG VGFGPLIITN SHLFKMNNGT 2100
LFVRSHQGEF TVQNTTQLQI YHVKDKDMIL IRMPKDFPPF PMKLKFRAPH 2150
SEERACLVGS RFQQKSLSSE VSDSTLIRPT DSGSGYWKHW VSTKEGDCGL 2200
PMVALKDGSL IGIHGLTSVR SELNYFVPFT DDFQSKYLSN IESLEWVKHW 2250
RHTPDKVAWN GMTLRENGPA SEFSVSKLIA DLTHGYVDEV VEQGYSSKWV 2300
ANRLDGNLKA VASSSSQLVT KHVVKGPCVL FQEFLATHEE AARYFVPRMG 2350
EYGPSRLNKE AFLKDFLKYA GPITVGVVNT NSFEDAVASV INMLEDLDYG 2400
ECAYVTDPDS IFDSLNMKAA VGALYKGKKK EYFEQLNTTE REDLLRLSCE 2450
RLYEGKMGVW NGSLKAELRP KEKLEQNKTR TFTAAPIDTL LGGKVCVDDF 2500
NNRFYSLNLK GPWSVGMTKF YGGWNELLQK LPDGWIYCDA DGSQFDSSLT 2550
PYLINAVVQI REHFMEDWEI GRTMLRNFYT EIVYTPILTP DGTIVKKFKG 2600
NNSGQPSTVV DNTLMVILAM HYAMHQQCWK EEEMKEKIRF FANGDDLLIA 2650
IYPSKEKFLN VLSEYFHELG LKYDFSSRST VRETLWFMSH RGLYLDDMYI 2700
PKLEEERIVS ILEWDRSNEA THRAEAICAA MIEAWGYPEL LKYIREFYLW 2750
MMQHECYRDL VRDGKLPYIA ETALRKLYTD KSVDENELVK YWKALAPEED 2800
DGPDIVTYQG DEKPSKSSQP QSSSPQVPQQ VDAGASSQGR DKQSVIKHDS 2850
TKSKDVGQSS TAVPRLKQIS KMRMPVSKGR QVLALDHLLD YKPEQVDLSN 2900
TRATKEQFDN WYEAVMREYD VSDSQMGVIM NGLMVWCIEN GTSPNLSGDW 2950
VMMDGEEQVS FPLKPIVENA KPSFRQIMHH FSDAAEAYIE MRNRERPYMP 3000
RYGAQRNLRD KTLARYAFDF YEVTSRTTDR AREAHFQMKA AALASVSNKL 3050
FGLDGSVATT SEDTERHTAT DVNAHMHHMM GVRQG 3085

Note: Produced by conventional translation.

Length:3,085
Mass (Da):349,731
Last modified:July 5, 2004 - v1
Checksum:i918576B242794C0D
GO
Isoform P3N-PIPO polyprotein (identifier: P0CJ96-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry P0CJ96.
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:1,038
Mass (Da):117,627
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY206394 Genomic RNA. Translation: AAP41071.1.
RefSeqiNP_954611.1. NC_005304.1. [Q6XW15-1]

Genome annotation databases

GeneIDi2943205.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY206394 Genomic RNA. Translation: AAP41071.1 .
RefSeqi NP_954611.1. NC_005304.1. [Q6XW15-1 ]

3D structure databases

ProteinModelPortali Q6XW15.
SMRi Q6XW15. Positions 2055-2269.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi S30.001.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 2943205.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR002540. Pept_S30_P1_potyvir.
IPR001456. Peptidase_C6.
IPR001592. Poty_coat.
IPR001730. Potyv_NIa-pro_dom.
IPR013648. PP_Potyviridae.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view ]
Pfami PF00270. 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 ]
PRINTSi PR00966. NIAPOTYPTASE.
SMARTi SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view ]
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEi 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 ]
ProtoNeti Search...

Publicationsi

  1. "The complete nucleotide sequence, genome organization, and specific detection of beet mosaic virus."
    Nemchinov L.G., Hammond J., Jordan R., Hammond R.W.
    Arch. Virol. 149:1201-1214(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. Cited for: REVIEW.

Entry informationi

Entry nameiPOLG_BTMV
AccessioniPrimary (citable) accession number: Q6XW15
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2005
Last sequence update: July 5, 2004
Last modified: September 3, 2014
This is version 81 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

External Data

Dasty 3

Similar proteinsi