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Genome polyprotein [Cleaved into: P1 proteinase (EC 3.4.-.-) (N-terminal protein); Helper component proteinase (HC-pro) (EC 3.4.22.45); Protein P3; 6 kDa protein 1 (6K1); Cytoplasmic inclusion protein (CI) (EC 3.6.4.-); 6 kDa protein 2 (6K2); Viral genome-linked protein (VPg); Nuclear inclusion protein A (NI-a) (NIa) (EC 3.4.22.44) (49 kDa proteinase) (49 kDa-Pro) (NIa-pro); Nuclear inclusion protein B (NI-b) (NIb) (EC 2.7.7.48) (RNA-directed RNA polymerase); Capsid protein (CP) (Coat protein)]

 POLG_BVY3               Reviewed;        3491 AA.
A0AUJ5;
30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
28-NOV-2006, sequence version 1.
23-MAY-2018, entry version 80.
RecName: Full=Genome polyprotein;
Contains:
RecName: Full=P1 proteinase;
EC=3.4.-.-;
AltName: Full=N-terminal protein;
Contains:
RecName: Full=Helper component proteinase;
Short=HC-pro;
EC=3.4.22.45;
Contains:
RecName: Full=Protein P3;
Contains:
RecName: Full=6 kDa protein 1;
Short=6K1;
Contains:
RecName: Full=Cytoplasmic inclusion protein;
Short=CI;
EC=3.6.4.-;
Contains:
RecName: Full=6 kDa protein 2;
Short=6K2;
Contains:
RecName: Full=Viral genome-linked protein;
AltName: Full=VPg;
Contains:
RecName: Full=Nuclear inclusion protein A;
Short=NI-a;
Short=NIa;
EC=3.4.22.44;
AltName: Full=49 kDa proteinase;
Short=49 kDa-Pro;
AltName: Full=NIa-pro;
Contains:
RecName: Full=Nuclear inclusion protein B;
Short=NI-b;
Short=NIb;
EC=2.7.7.48;
AltName: Full=RNA-directed RNA polymerase;
Contains:
RecName: Full=Capsid protein;
Short=CP;
AltName: Full=Coat protein;
Blackberry virus Y (isolate Blackberry plant/USA:Arkansas/C3ARK/2005)
(BVY).
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage;
Potyviridae; Brambyvirus.
NCBI_TaxID=686949;
NCBI_TaxID=211815; Rubus plicatus.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
PubMed=17933412; DOI=10.1016/j.virusres.2007.09.001;
Susaimuthu J., Tzanetakis I.E., Gergerich R.C., Martin R.R.;
"A member of a new genus in the Potyviridae infects Rubus.";
Virus Res. 131:145-151(2008).
-!- FUNCTION: 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. {ECO:0000250}.
-!- FUNCTION: Nuclear inclusion protein B: an RNA-dependent RNA
polymerase that plays an essential role in the virus replication.
{ECO:0000250}.
-!- FUNCTION: 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). {ECO:0000250}.
-!- FUNCTION: Cytoplasmic inclusion protein: has helicase activity. It
may be involved in replication (By similarity). {ECO:0000250}.
-!- FUNCTION: Both 6K peptides are indispensable for virus
replication. {ECO:0000250}.
-!- FUNCTION: Nuclear inclusion protein A: has RNA-binding and
proteolytic activities. {ECO:0000250}.
-!- CATALYTIC ACTIVITY: 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.
-!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
+ RNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00539}.
-!- CATALYTIC ACTIVITY: 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.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
Evidence={ECO:0000255|PROSITE-ProRule:PRU00805};
Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000255|PROSITE-
ProRule:PRU00805};
-!- SUBCELLULAR LOCATION: Capsid protein: Virion {ECO:0000305}.
-!- DOMAIN: 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). {ECO:0000250}.
-!- PTM: 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). {ECO:0000250}.
-!- PTM: 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).
{ECO:0000250}.
-!- SIMILARITY: Belongs to the potyviridae genome polyprotein family.
{ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AY994084; AAX87001.1; -; Genomic_RNA.
RefSeq; YP_851006.1; NC_008558.1.
ProteinModelPortal; A0AUJ5; -.
PRIDE; A0AUJ5; -.
GeneID; 5076635; -.
KEGG; vg:5076635; -.
OrthoDB; VOG090001ZS; -.
Proteomes; UP000006703; Genome.
GO; GO:0019029; C:helical viral capsid; IEA:UniProtKB-KW.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003723; F:RNA binding; IEA:InterPro.
GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
GO; GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
Gene3D; 2.60.120.590; -; 1.
InterPro; IPR037151; AlkB-like_sf.
InterPro; IPR001456; HC-pro.
InterPro; IPR031159; HC_PRO_CPD_dom.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR005123; Oxoglu/Fe-dep_dioxygenase.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR002540; Pept_S30_P1_potyvir.
InterPro; IPR009003; Peptidase_S1_PA.
InterPro; IPR001592; Poty_coat.
InterPro; IPR001730; Potyv_NIa-pro_dom.
InterPro; IPR013648; PP_Potyviridae.
InterPro; IPR001205; RNA-dir_pol_C.
InterPro; IPR007094; RNA-dir_pol_PSvirus.
Pfam; PF00271; Helicase_C; 1.
Pfam; PF00863; Peptidase_C4; 1.
Pfam; PF00851; Peptidase_C6; 1.
Pfam; PF01577; Peptidase_S30; 1.
Pfam; PF00767; Poty_coat; 1.
Pfam; PF08440; Poty_PP; 1.
Pfam; PF00680; RdRP_1; 1.
PRINTS; PR00966; NIAPOTYPTASE.
SMART; SM00487; DEXDc; 1.
SMART; SM00490; HELICc; 1.
SUPFAM; SSF50494; SSF50494; 1.
SUPFAM; SSF52540; SSF52540; 1.
PROSITE; PS51471; FE2OG_OXY; 1.
PROSITE; PS51744; HC_PRO_CPD; 1.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
PROSITE; PS51436; POTYVIRUS_NIA_PRO; 1.
PROSITE; PS50507; RDRP_SSRNA_POS; 1.
3: Inferred from homology;
ATP-binding; Capsid protein; Complete proteome;
Covalent protein-RNA linkage; Dioxygenase; Helical capsid protein;
Helicase; Hydrolase; Iron; Metal-binding; Nucleotide-binding;
Nucleotidyltransferase; Oxidoreductase; Phosphoprotein; Protease;
Reference proteome; RNA-directed RNA polymerase;
Suppressor of RNA silencing; Thiol protease; Transferase;
Viral RNA replication; Virion.
CHAIN 1 3491 Genome polyprotein.
/FTId=PRO_0000419995.
CHAIN 1 745 P1 proteinase.
/FTId=PRO_5000147981.
CHAIN 746 1070 Helper component proteinase.
/FTId=PRO_5000147982.
CHAIN 1071 1420 Protein P3.
/FTId=PRO_5000147983.
CHAIN 1421 1476 6 kDa protein 1.
/FTId=PRO_5000147984.
CHAIN 1477 2096 Cytoplasmic inclusion protein.
/FTId=PRO_5000147985.
CHAIN 2097 2163 6 kDa protein 2.
/FTId=PRO_5000147986.
CHAIN 2164 2353 Viral genome-linked protein.
/FTId=PRO_5000147987.
CHAIN 2354 2590 Nuclear inclusion protein A.
/FTId=PRO_5000147988.
CHAIN 2591 3143 Nuclear inclusion protein B.
/FTId=PRO_5000147989.
CHAIN 3144 3491 Capsid protein.
/FTId=PRO_5000147990.
DOMAIN 183 277 Fe2OG dioxygenase. {ECO:0000255|PROSITE-
ProRule:PRU00805}.
DOMAIN 948 1070 Peptidase C6. {ECO:0000255|PROSITE-
ProRule:PRU01080}.
DOMAIN 1540 1692 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 1696 1869 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
DOMAIN 2354 2570 Peptidase C4. {ECO:0000255|PROSITE-
ProRule:PRU00766}.
DOMAIN 2850 2974 RdRp catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00539}.
NP_BIND 1553 1560 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 1642 1645 DEAH box.
COMPBIAS 2594 2597 Poly-Thr.
COMPBIAS 3166 3170 Poly-Gln.
ACT_SITE 956 956 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 1029 1029 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 2400 2400 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2435 2435 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2504 2504 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
METAL 201 201 Iron. {ECO:0000255|PROSITE-
ProRule:PRU00805}.
METAL 203 203 Iron. {ECO:0000255|PROSITE-
ProRule:PRU00805}.
METAL 259 259 Iron. {ECO:0000255|PROSITE-
ProRule:PRU00805}.
BINDING 268 268 2-oxoglutarate. {ECO:0000255|PROSITE-
ProRule:PRU00805}.
SITE 745 746 Cleavage; by P1 proteinase.
{ECO:0000255}.
SITE 1070 1071 Cleavage; by autolysis.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
SITE 1420 1421 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1476 1477 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2096 2097 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2163 2164 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2353 2354 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2590 2591 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 3143 3144 Cleavage; by NIa-pro. {ECO:0000250}.
MOD_RES 2238 2238 O-(5'-phospho-RNA)-tyrosine.
{ECO:0000250}.
SEQUENCE 3491 AA; 393838 MW; E548F95E522B9155 CRC64;
MPTRYRGADR YGNLGYDKVL QSKADAAKRR GLLFDHGSET YECPRCGEIW RNLDDYMAEG
GKMHPKKCLP EECDSDEEQI SSCNAALIHE KWGDLDSDTS SKLSEFYKEP SILTYTTRTH
CVVEKMRSMT APQCIEDIVG VRLHGRTAWF FSKDPTLQYG HHPIYYDTHP WNDELDKYLG
GAKYNTALVQ VYDGTRDLPY HKDDEPCYDI TNNPIRTVNV TGTGDLCISK DKRRLYETIP
MTSGTVITFP ATMQENFYHA VRNPSAGRIS ITFRNQIRTV ERQVAHSANK RWVPIVEARV
TTNESRRGDN KQFQEAQSKL QTKTTINFGE FAAEVDGYYP TLSQDHKPAL PKIIPELGLP
TVDFIYVGNM RVPIDFKKNN VPAIVDTARH VAKIIDSQAL TSEPIKVFTE QREVVGNVVT
CTGTGFSVAD AKEAKALLNG LMYNRASNLF ICPSCSDAAV LPEALLTLEH KRSCELASMK
KISLARNMQV HVKQEAVARL ISQQNSISVP IATLSSCVRG SADTTQVSLH IDEEDSIVDA
IHLPNDFITC DHEHAFETDS ASDNDVETMK KSEKRRKRRK RNPPPVRQVI TRAPVSNIIC
DVILTCLETQ IPVEFIGKSC ITFKPVRVGP VHTVGIQLKH QLHKTGFEVD DLPDRETTSD
IILAATRALR RLRHAHSNAQ QVHNSDITFG TSGAILPWSW LAHDVIVEGP VQDSLVVRGR
NVVSGHVTNA LNLQQDCLAD DYLQYSEELQ PLHDDLSELK PLNVINNELI RQNMHITTLY
SNMSKLQNDA LATKAEMKLP LFGVAQLVVN QLKYNTTTHE WGERGDYVRK FVGKFFADFP
TTQVPKQYMT RTTNGHIRIT AYKALSLTSD PEIMMSRRMT QPMLTTAKQA DCVFQSTTGA
TCTSASCTTN SSGVVLSNKC ADPAPNTLRV RTMWDDIIIE LPLQGGRVHV PLEGLCFSTI
FLHMYLLVPD ESVKLFHRTV TERAMPSLGQ WPTLRHLATW VLNLVAMFPV LSTTPMPEIL
VHHESQSVHI PDCLGTATSG YHRLNIVTPY DFIIFATEIG RNGCQEYRVG GFAHDIKYTV
SLMQDKRKLL HELMLTPTWA FYALSSPTLL KILYRSGALK RTYEHAVMAN HNAVDLVHEL
NFLPERVSRA QTLQDEITAW EANVGRVLQQ VDGYLTRNHD PPLQRWYADA SARLQHLKID
VDLLKNGFRS SQREHVEKKE QLLCDSFERL YNEQNSSLES LKTRCGMGSA RALIKPSGKC
ESPEPAKQLS CKDLICSTKD KYALMLYTQA DALKRKIVAG SQSAFTTVCA GVAYRATKVM
LRTPFNLLNA LNTYSLLIAA VNVMVLVQNY RRDQRKRAQY VNNLETQSMI RHYFAHLEQY
IVNYVPRDEQ FEVIKAKFDE EFPEYNVMFK EVYKERIQFQ SADEGKNMCK IFASAILVMM
VFDAHRADLM YKSFSQVRAL FNTLYDSGNP FNIIFQAERT IAPTMDVIIQ EPKPAIPSTS
SCTFETWFRN CVNANNVIPV IPECDLLDFT RDTASSVVAT LTSSVKREFV IRGFVGSGKS
TYLPHLLTKH GKVLLCEPVR VLASNVFEAL SGSPFYQSPT LLMRGTTKFG SGKITVATSG
YAANYYNANR HRLNEFAYII FDESHQHTAH NFLLRSILDV IGYEGTVLHV SATPIGKEIP
FRTMHPVEVV NMSTLSFEDF AIGQRKQVRC DVFNKGANIL VYVASYNDVD RMSTLLLERG
LRVKKIDART VANVNNITCD GSDGEPLYLV ATNIVENGVT LNVDVVVDFG LCVKPVINAL
QRRVDYVKTP ITWGQRIQRN GRVGRYKNGF CLNVGDVYKT PPIISEDVAL ESALMCFAAN
VPPIFDNVDP ALFGQVTRPQ VQTAQMFELP IYITTPMISD AGALQSDIYQ VIKKFVLREG
SIQLTQDATY LSNMSNWKTI ADYFPDISDT HAMRHEKVPF FVKDFGENSY IALAEAIRKA
RNKSLGARGK LYGDVDATAL LLQTDPGSLD RSIMIVETEL VAQRSKLEDL NHHVHESTGM
FQRYVSHLNH CLRGRYQTDQ IQKNIEVLSN MRSTLVGYRQ VVDKVEPEEI PHFVQQNPNI
TMIIDFQSDR TKADGFVKHG INGIYNYTKI ASDTFSLLLI ACVVIYYVVQ YFFREMKSHI
TFEASGSRRN RLHLRDNKLI KGGYTWAGPS DDMEREFGPE YALKRDKFSE KKARKHMRER
IQPRTNMGVK LAPFQVFYGF DVADYDVLQL FDPITGVKID MDPRATAKEI TEEVEDTPFN
KEVWSDTHMP EKIQATFVKK GGVNREDVLK QVRVDMTTHN PTMVTGSGGI MGYPEHKGDF
RQTGPPKFSI VPEGRSTIKS GNNIAPFISA MGTIKNVYMN GDFDTLACTQ IGNKLVVNAH
IFMEPVKKQE LILQHGVYEL PNNGTINIKH VPGIDMVIQT LPMDVPLARQ IKAYRGPIPG
ELIRLLKIER NTKTNSTSLS DPGTARVGPG TIWYHNITTK HGDCGSLVLS EKDNKIVGIH
TGQQDGTNLN LFAPITKDAI VAIETVLPGE LNDWVFTPDM LDVGSNNAIR KQASDPFPVV
KKLLEGITFQ NNRTTTTDSV SNTAILPARK YWVASDLPVN IKYQCDMPTF FNTRHTYEGE
SQPFMAYLRE CGDAETFFRP LLSHYIPSNL NGDAFKKDFF KYGKPVPVGL VHGPSFKIAS
DRVIKRFERV GYERHSIPFE FDAEAIRDDL NKHAAMGAQY VGKKEQHLDG ISEEQFCDEF
VASCCRLANN CDGVWKGSLK AELRSKEKVQ ENKTRVFTSA PYDVLLGGKA CVMHFNKKFY
ANNTKGPWTV GINKLGLGWH RLLKSLPEGF VYGTGDGSQF DSSLTPLLIN EVCRIRMYFM
QDDELGQAML RGLYRQIIWT LISMPDGSVV RKAKGNPSGQ PSTVDDNTIM VMLAVEYVFA
YLGITQEEMD TIFKYYANGD DLIFAIHPDR ESILNEFTHL FAHLGLNYIF EDRTRNRAEL
EYMSLTGIER EGFYIPKLSR ERISSIVQWR RKGDTRAMFD ALNAAILESW GYDDLTYWLR
KYYEWLIINR YDIDLPEGEK LPYHTETAVE TLYTCDDNTT VYDGRYDFEV PTDASGGVFI
IDFQSSSGTD TPPVIPPATS EPALQPVLTR QTSRPPTPPN TILTGQQQQQ LMPKSSQPYQ
LEPLLAPTGV QQPTFGTFGM PQAQQTTTEP VVAAARVRGK QKEGDTSLSQ VRDHRRLSPE
RIVRHDDDLA PPNESTSGES SHYDELTLPD VPRDKRKGLG ARLKGKPIIT QTQIYNYRPA
FGSIHNNKAT DIELEAWKKQ IADYFQVDDV STLILGFMAY VIENGTSPEI FTNQKFVMAT
SSGEQREYPL APFRSRSVEL RKIMRRFSEE AIDYIQIQRE HNPQYVPRQA VVRNVKRAIY
FPYCFDFIDE TILTPDALEI VHQMKAAALE SASSKVLGLD GGSARAIDTE RHTTEDATAR
THNLRGAAMM A


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