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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_TUMVQ              Reviewed;        3163 AA.
Q02597;
01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
01-JUN-1994, sequence version 2.
25-OCT-2017, entry version 139.
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;
Turnip mosaic virus (strain Quebec) (TuMV).
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage;
Potyviridae; Potyvirus.
NCBI_TaxID=36396;
NCBI_TaxID=126269; Alliaria.
NCBI_TaxID=3705; Brassica.
NCBI_TaxID=38206; Calanthe.
NCBI_TaxID=3719; Capsella bursa-pastoris (Shepherd's purse) (Thlaspi bursa-pastoris).
NCBI_TaxID=264418; Hesperis matronalis.
NCBI_TaxID=13274; Stellaria media (Common chickweed) (Alsine media).
NCBI_TaxID=74517; Trifolium hybridum (Alsike clover).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
PubMed=1431807; DOI=10.1099/0022-1317-73-11-2785;
Nicolas O., Laliberte J.F.;
"The complete nucleotide sequence of turnip mosaic potyvirus RNA.";
J. Gen. Virol. 73:2785-2793(1992).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1534-3163, AND PARTIAL PROTEIN
SEQUENCE.
PubMed=2254757; DOI=10.1099/0022-1317-71-11-2769;
Tremblay M.F., Nicolas O., Sinha R., Lazure C., Laliberte J.F.;
"Sequence of the 3'-terminal region of turnip mosaic virus RNA and the
capsid protein gene.";
J. Gen. Virol. 71:2769-2772(1990).
[3]
REVIEW.
PubMed=11226583; DOI=10.1016/S0168-1702(01)00220-9;
Urcuqui-Inchima S., Haenni A.L., Bernardi F.;
"Potyvirus proteins: a wealth of functions.";
Virus Res. 74:157-175(2001).
-!- 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.
-!- FUNCTION: Nuclear inclusion protein B: an RNA-dependent RNA
polymerase that plays an essential role in the virus replication.
-!- 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.
-!- 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.
-!- SUBCELLULAR LOCATION: Capsid protein: Virion {ECO:0000305}.
-!- ALTERNATIVE PRODUCTS:
Event=Ribosomal frameshifting; Named isoforms=2;
Name=Genome polyprotein;
IsoId=Q02597-1; Sequence=Displayed;
Note=Produced by conventional translation.;
Name=P3N-PIPO polyprotein;
IsoId=P0CK12-1; Sequence=External;
Note=Produced by -1 ribosomal frameshifting in P3 ORF.;
-!- 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.
-!- 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: 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). {ECO:0000250}.
-!- SIMILARITY: Belongs to the potyviridae genome polyprotein family.
{ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; D10927; BAA01725.1; -; Genomic_RNA.
EMBL; D10601; BAA01452.1; -; Genomic_RNA.
PIR; JQ1895; JQ1895.
ProteinModelPortal; Q02597; -.
MEROPS; C06.001; -.
OrthoDB; VOG0900003L; -.
Proteomes; UP000008263; 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:0004386; F:helicase activity; 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.
CDD; cd00079; HELICc; 1.
InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
InterPro; IPR001456; HC-pro.
InterPro; IPR031159; HC_PRO_CPD_dom.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
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; PF00270; DEAD; 1.
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; 2.
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.
1: Evidence at protein level;
ATP-binding; Capsid protein; Complete proteome;
Covalent protein-RNA linkage; Direct protein sequencing;
Helical capsid protein; Helicase; Hydrolase; Nucleotide-binding;
Nucleotidyltransferase; Phosphoprotein; Protease;
Ribosomal frameshifting; RNA-directed RNA polymerase;
Suppressor of RNA silencing; Thiol protease; Transferase;
Viral RNA replication; Virion.
CHAIN 1 3163 Genome polyprotein.
/FTId=PRO_0000420030.
CHAIN 1 362 P1 proteinase. {ECO:0000255}.
/FTId=PRO_0000040473.
CHAIN 363 820 Helper component proteinase.
{ECO:0000255}.
/FTId=PRO_0000040474.
CHAIN 821 1175 Protein P3. {ECO:0000250}.
/FTId=PRO_0000040475.
CHAIN 1176 1227 6 kDa protein 1. {ECO:0000250}.
/FTId=PRO_0000040476.
CHAIN 1228 1870 Cytoplasmic inclusion protein.
{ECO:0000250}.
/FTId=PRO_0000040477.
CHAIN 1871 1923 6 kDa protein 2. {ECO:0000250}.
/FTId=PRO_0000040478.
CHAIN 1924 2115 Viral genome-linked protein.
{ECO:0000250}.
/FTId=PRO_0000040479.
CHAIN 2116 2358 Nuclear inclusion protein A.
{ECO:0000250}.
/FTId=PRO_0000040480.
CHAIN 2359 2875 Nuclear inclusion protein B.
{ECO:0000250}.
/FTId=PRO_0000040481.
CHAIN 2876 3163 Capsid protein. {ECO:0000250}.
/FTId=PRO_0000040482.
DOMAIN 698 820 Peptidase C6. {ECO:0000255|PROSITE-
ProRule:PRU01080}.
DOMAIN 1300 1452 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 1471 1630 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
DOMAIN 2116 2334 Peptidase C4. {ECO:0000255|PROSITE-
ProRule:PRU00766}.
DOMAIN 2600 2724 RdRp catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00539}.
NP_BIND 1313 1320 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 414 417 Involved in interaction with stylet and
aphid transmission. {ECO:0000250}.
MOTIF 672 674 Involved in virions binding and aphid
transmission. {ECO:0000250}.
MOTIF 1402 1405 DECH box.
MOTIF 1964 1971 Nuclear localization signal.
{ECO:0000255}.
ACT_SITE 270 270 For P1 proteinase activity.
{ECO:0000250}.
ACT_SITE 279 279 For P1 proteinase activity.
{ECO:0000255}.
ACT_SITE 313 313 For P1 proteinase activity.
{ECO:0000250}.
ACT_SITE 706 706 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 779 779 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 2161 2161 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2196 2196 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2266 2266 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
SITE 362 363 Cleavage; by P1 proteinase.
{ECO:0000255}.
SITE 820 821 Cleavage; by autolysis.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
SITE 1175 1176 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1227 1228 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1870 1871 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2115 2116 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2358 2359 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2875 2876 Cleavage; by NIa-pro. {ECO:0000250}.
MOD_RES 1986 1986 O-(5'-phospho-RNA)-tyrosine.
{ECO:0000250}.
CONFLICT 2862 2862 E -> G (in Ref. 2; BAA01452).
{ECO:0000305}.
SEQUENCE 3163 AA; 357822 MW; 61B0F73B58DF6D59 CRC64;
MAAVTFASAI TNAITNKTTS TGMVQFGSFP PMPLRSTTVT TVATPVGQPK LYTVRFGSLD
PVIVKGGAGS LAKATRQQPS VEIDVSLSEA AALEVAKPKS SAVLRMHEEA NKERALFLDW
EASLKRRSYG IAENEKVVMT TRGVSKIVPR SSRAMKQKRA RERRRAQQPI ILKWEPKLSG
FSIGGGFSAS AIEAEEVRTK WPLHKTPSMK KRMVHKTCKM SDQGVDMLIR SLVKIFKAKS
ANIEYIGKKP IKVDFIRKER TKFARIQVAH LLGKRAQRDL LAGMEENHFI DILSEYSGNG
TTINPGVVCA GWSGIVVRNE TLTQKRSRSP SKAFVIRGEH EDKLYDARIK ITKTMSLKIV
HFSARGANFW KGFDRCFLAY RSDNREHTCY SGLDVTECGE VAALMCLAMF PCGKITCPDC
VIDSELSQGQ ASGPSMKHRL TQLRDVIKSS YPRFKHAVQI LDRYEQSLSS ANENYQDFAE
IQSISDGVEK AAFPHVNKLN AILIKGATAT GEEFSQATKH LLEIARYLKN RTENIEKGSL
KSFRNKVSQK AHINPTLMCD NQLDKNGNFI WGERGYHAKR FFSNYFEIID PKKGYTQYET
RVVPNGSRKL AIGKLIVPTN FEVLREQMRG EPVEPYPVTV ECVSKSQGDF VHACCCVTTE
SGDPVLSEIK MPTKHHLVIG NSGDPKYIDL PEIEENKMYI AKEGYCYINI FLAMLVNVKE
SQAKEFTKVV RDKLVSELGK WPTLLDVATA CYFLKVFYPD VANAELPRML VDHKTKIIHV
VDSYGSLSTG YHVLKTNTVE QLIKFTRCNL ESSLKHYRVG GTEWENAHGA DNIDNPQWCI
KRLVKGVYRP KQLKEDMLAN PFLPLYALLS PGVILAFYNS GSLEHLMNHY ISADSNVAVL
LVVLKSLAKK VSTSQSVLAQ LQIIERSLPE LIEAKANING PDDAATRACN RFMGMLLHMA
EPNYELANGG YTFLRDHSIS ILEKSYLQIL DEAWNELSWS ERCVIRYYPS KQAIFTQKDL
PMQSEADLGG RYSESVISSY EWSKQQAKGV KDSVVNKLRS SMSWTSSKVS NSVCRTINYL
VPDVFKFMNV LVCISLLIKM TAEANHIITT QRRLKLDIEE TERKKIEWEL AFHHNILTHS
ASQHPTLDEF TAYIAEKAPH LSEHIEPEEK EVVHQAKRQS EQELERVIAF VALVLMMFDA
ERSDCVTKIL NKLKGLVATV EPTVYHQTLN EIEDDLNERN LFVDFELSSD SEMLQQLPAE
KTFASWWSHQ LSRGFTIPHY RTEGKFMTFT RATATEVAGK IAHESDKDIL LMGAVGSGKS
TGLPYHLSRK GNVLLLEPTR PLAENVHKQL SQAPFHQNTT LRMRGLTAFG SAPISVMTSG
FALNYFANNR SRIEEFDFVI FDECHVHDAN AMAMRCLIHE CDYSGKIIKV SATPPGREVE
FSTQYPVSIS TEDTLSFQDF VNAQGSGSNC DVISKGDNIL VYVASYNEVD TLSKLLIERD
FKVTKVDGRT MKVGNIEITT SGTPSRKHFI VATNIIENGV TLDIDVVADF GTKVLPYLDT
DNRMLSTTKT SINYGERIQR LGRVGRHKPG HALRIGHTER GLSEVPSCIA TEAALKCFTY
GLPVITNNVS TSILGNVTVK QARTMSVFEI TPFYTSQVVR YDGSMHPQVH ALLKRFKLRD
SEIVLTKLAI PNRGVNAGSQ PVSMHDSVQM LKIGVTLRIP FMCRDIPEKL HLDMWDVVVK
FKGDAGFGRL SSSASKVAYT LQTDVNSIQR TVTIIDTLIA EERRKQEYFK TVTSNCVSSS
NFSLQSITNA IKSRMMKDHP CENISVLEGA KSQLLEFRNL NSDHSFVTKT DGISRSFMRD
YGALEAVNHQ STNEMSKFLQ LKGKWNKTLI TRDVLVICGV LGGGVWMVVQ HFRSKVSEPV
THEAKGKKQR QKLKFRNARD NKMGREVYGD DDTIEHFFGD AYTKKGKSKG RTRGIGHKNR
KFINMYGFDP EDFSAVRFVD PLTGATLDDN PFTDITLVQK HFGDIRMDLL GEDELDSNEI
RMNKTIQAYY MNNKTGKALK VDLTPHIPLK VCDLHATIAG FPERENELRQ TGKAQPINID
EVPRANNELV PVDHESNSMF RGLRDYNPIS NNICHLTNVS DGASNSLYGV GFGPLILTNR
HLFERNNGEL IIKSRHGEFV IKNTTQLHLL PIPDRDLLLI RLPKDVPPFP QKLGFRQPEK
GERICMVGSN FQTKSITSIV SETSTIMPVE NSQFWKHWIS TKDGQCGSPM VSTKDGKILG
LHSLANFQNS INYFAAFPDD FTEKYLHTIE AHEWVKHWKY NTSAISWGSL NIQASQPVSL
FKVSKLISDL DSTAVYAQTQ QNRWMFEQLT GNLKAIAHCP SQLVTKHTVK GKCQMFDLYL
KLHDEAREYF QPMLGQYQKS KLNREAYAKD LLKYATPIEA GNIDCDLFEK TVEIVISDLR
GYGFETCNYV TDENDIFEAL NMKSAVGALY KGKKKDYFAE FTPEVKEEIL KQSCERLFLG
KMGVWNGSLK AELRPLEKVE ANKTRTFTAA PLDTLLGGKV CVDDFNNQFY DHNLRAPWDV
GMTKFYCGWD RLLESLPDGW VYCDADGSQF DSSLSPYLIN AVLNIRLGFM EEWDVGEVML
RNLYTEIVYT PISTPDGTLV KKFKGNNSGQ PSTVVDNTLM VILAVNYSLK KGGIPSELRD
SIIRFFVNGD DLLLSVHPEY EYILDTMADN FRELGLKYTF DSRTREKGDL WFMSHQGHRR
EGIWIPKLEP ERIVSILEWD RSKEPCHRLE AICAAMIESW GYDKLTHEIR KFYAWMIEQA
PFSSLAQEGK APYIAETALR KLYLDKEPAQ EDLTQYLQAI FEDYEDGVEA CVYHQAGETL
DADLTEEQKQ AEKEKKEREK AEKERERQKQ LAFKKGKDVA QEEGKRDKEV NAGTSGTFSV
PRLKSLTSKM RVPRYEKRVA LNLDHLILYT PEQTDLSNTR STRKQFDTWF EGVMADYELT
EDKMQIILNG LRVWCIENGT SPNINGMWVM MDGDDQVEFP IKPLIDHAKP TFRQIMAHFS
DVAEAYIEKR NQDRPYMPRY GLQRNLTDMS LARYAFDFYE MTSRTPIRAR EAHIQMKAAA
LRGANNNLFG LDGNVGTTVE NTERHTTEDV NRNMHNLLGV QGL


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