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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_LMVE               Reviewed;        3255 AA.
P89876;
15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
01-MAY-1997, sequence version 1.
25-OCT-2017, entry version 134.
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;
Lettuce mosaic virus (strain E) (LMV).
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage;
Potyviridae; Potyvirus.
NCBI_TaxID=117131;
NCBI_TaxID=4222; Carthamus tinctorius (Safflower).
NCBI_TaxID=3827; Cicer arietinum (Chickpea) (Garbanzo).
NCBI_TaxID=114280; Cichorium endivia (Endive).
NCBI_TaxID=13427; Cichorium intybus (Chicory).
NCBI_TaxID=52518; Eustoma exaltatum subsp. russellianum (Bluebells) (Eustoma grandiflorum).
NCBI_TaxID=4235; Lactuca.
NCBI_TaxID=3888; Pisum sativum (Garden pea).
NCBI_TaxID=3562; Spinacia oleracea (Spinach).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
PubMed=9085548; DOI=10.1016/S0168-1702(96)01411-6;
Revers F., Yang S.J., Walter J., Souche S., Lot H., Le Gall O.,
Candresse T., Dunez J.;
"Comparison of the complete nucleotide sequences of two isolates of
lettuce mosaic virus differing in their biological properties.";
Virus Res. 47:167-177(1997).
[2]
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.
-!- 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=P89876-1; Sequence=Displayed;
Note=Produced by conventional translation.;
Name=P3N-PIPO polyprotein;
IsoId=P0CW79-1; 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; X97705; CAA66281.1; -; Genomic_RNA.
RefSeq; NP_619667.1; NC_003605.1.
ProteinModelPortal; P89876; -.
GeneID; 940180; -.
KEGG; vg:940180; -.
OrthoDB; VOG0900003L; -.
Proteomes; UP000008378; 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.
3: Inferred from homology;
ATP-binding; Capsid protein; Complete proteome;
Covalent protein-RNA linkage; 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 3255 Genome polyprotein.
/FTId=PRO_0000420000.
CHAIN 1 437 P1 proteinase. {ECO:0000255}.
/FTId=PRO_0000040279.
CHAIN 438 895 Helper component proteinase.
{ECO:0000255}.
/FTId=PRO_0000040280.
CHAIN 896 1273 Protein P3. {ECO:0000250}.
/FTId=PRO_0000040281.
CHAIN 1274 1325 6 kDa protein 1. {ECO:0000250}.
/FTId=PRO_0000040282.
CHAIN 1326 1968 Cytoplasmic inclusion protein.
{ECO:0000250}.
/FTId=PRO_0000040283.
CHAIN 1969 2021 6 kDa protein 2. {ECO:0000250}.
/FTId=PRO_0000040284.
CHAIN 2022 2214 Viral genome-linked protein.
{ECO:0000250}.
/FTId=PRO_0000040285.
CHAIN 2215 2457 Nuclear inclusion protein A.
{ECO:0000250}.
/FTId=PRO_0000040286.
CHAIN 2458 2977 Nuclear inclusion protein B.
{ECO:0000250}.
/FTId=PRO_0000040287.
CHAIN 2978 3255 Capsid protein. {ECO:0000250}.
/FTId=PRO_0000040288.
DOMAIN 773 895 Peptidase C6. {ECO:0000255|PROSITE-
ProRule:PRU01080}.
DOMAIN 1397 1549 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 1568 1727 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
DOMAIN 2215 2433 Peptidase C4. {ECO:0000255|PROSITE-
ProRule:PRU00766}.
DOMAIN 2699 2823 RdRp catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00539}.
NP_BIND 1410 1417 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 489 492 Involved in interaction with stylet and
aphid transmission. {ECO:0000250}.
MOTIF 747 749 Involved in virions binding and aphid
transmission. {ECO:0000250}.
MOTIF 1499 1502 DECH box.
MOTIF 2062 2069 Nuclear localization signal.
{ECO:0000255}.
COMPBIAS 1266 1271 Poly-Glu.
COMPBIAS 2965 2972 Poly-Asp.
ACT_SITE 345 345 For P1 proteinase activity.
{ECO:0000250}.
ACT_SITE 354 354 For P1 proteinase activity.
{ECO:0000255}.
ACT_SITE 388 388 For P1 proteinase activity.
{ECO:0000250}.
ACT_SITE 781 781 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 854 854 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 2260 2260 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2295 2295 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2365 2365 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
SITE 437 438 Cleavage; by P1 proteinase.
{ECO:0000255}.
SITE 895 896 Cleavage; by autolysis.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
SITE 1273 1274 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1325 1326 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1968 1969 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2021 2022 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2214 2215 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2457 2458 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2977 2978 Cleavage; by NIa-pro. {ECO:0000250}.
MOD_RES 2084 2084 O-(5'-phospho-RNA)-tyrosine.
{ECO:0000250}.
SEQUENCE 3255 AA; 367624 MW; B3E8582927E01628 CRC64;
MATLDNCTQV HHMFAYNREH GTNYTRNHFR RYLAAQRIGF YYDWDDDVYE CPTCEAIYHS
LDEIKNWHEC DPPAFDLNDF ITDARLKSAP VPDLGPVIVE TPKVEEKQEL NFFAATPAPE
VLQWKCRGLQ FGSFTELETS EPVVSAPKPN CEEPARTIAK PEEPVEQETC GDGKRLLQAQ
MEVDKAEQDL AFAYLSASLK PRLEGRTTAT IARRRDGCLV YKTKPSWSQR KGTKKILKVD
TLACKNPYIP AVVDKISIAG GSSASVMHEQ QKPKILHTTP SRKVATHYKR TVMNQQTLTA
LINQVGTIIL NAEKEFEVVG CRKQKVTGKG TRHNGVRLVK LKTAHEEGHR RKVDIRIPNG
LRSIVTRISA RGGWHKTWTD SELSPGSSGY VLNSSKIIGE FGLRRHSIFV VRGRVYGKII
DSQSKVTHTL THRMVQYSDV ARNFWNGYST CFMHNTPKDI LHTCTSDFDV KDCGTVAALL
TQTLFQFGKI TCGKCAIEYK NLTRDELATR VNKEIDGTII SIQTQHPRFV HVLNFLRLIK
QVLNAKNGNF GAFQETERII GDRMDAPFSH VNKLNAIVIK GNQATSDEMA QASNHVLEIA
RYFKNRTENI QKGSLKSFRN KISGKAHLNP SLMCDNQLDK NGGFEWGQRS YHAKRFFDGY
FETIDPSDGY SKYTIRRNPN GHRKLAIGNL IVSTNFESHR RSMVGEPIED PGLTNQCVSK
EGGAFIYPCC CVTDEYGKPT LSEIKMPTKH HLVLGNAGDP KYVDLPKEAE GKMFVAKDGY
CYINIFLAML VDVPEDQAKD FTKMAREIAV KQLGEWPSMM DVATACNILA TFHPDTRRSE
LPRILVDHAT KTFHVIDSYG SITTGYHILK ANTVTQLVKF AHESLESEMQ HYRVGGEPDK
APRKPAGNVP TLGISDLKNL GVESENEEHS IRPNLQRLIK AIYRPRMMRS LLTEEPYLLI
LSIVSPGVLM ALYNSGSLER TMHEFLQTDQ RLSATAQILK HLAKKVSLAK TLTIQNAILE
GGAGSLNEIL DAPAGRSLSY RLAKQTVEVM MARSDMDKEL VDVGFSVLRD QKNELIEKSY
LMDLEDSWRA LPLCGKLSAM RVSRRWRDTS TPEAIPTGAA DLKGRYSISV GSVSKSAILH
LKGICSGAVK RVKDKWVGVQ VQGVKWLAKS VHYMIPELTN ILNVGTLLLT LISLGVRFRS
LTGQFKEMKY KETLAREEEL RKRIRTYNST YYEIHGKHAD AKQITKFITH HDPKLLEVVE
FYEGPEEEEV EHQAKREDQA NLERIIAFTA LVMMMFDSER SDCVYRSLSK LKSLVSTCDD
DVRHQSVDEI IDLFDEKKET IDFEIEGKEL YSSRVVDSTF SKWWDNQLVR GNTMAHYRTE
GHFMTFTRET AASVAAEIAH NEYRDILLQG GVGSGKSTGL PFHLHKKGGV LLIEPTRPLA
QNVYKQLGSN PFHLSPNLRM RGACKFGSSQ VTVATSGYAL HFIANNAQSL KMFDFIIFDE
CHVLDASAMA FRCLLQEFEY QGKIIKVSAT PPGRKLDFKP MHMVDITTEN ELSIQQFVQG
QGTGVNCDAT KKGDNILVYV SSYNEVDMLS KMLNDKGYKV TKVDGRTMKL GSVEVETVGT
PQRKHFVVAT NIIENGVTLD VDVVVDFGQK VVPILDSEHR MIRYTKKSIT YGERIQRVGR
VGRNKAGSAI RIGSTEMGTE EIPASIATEA AFLCFTYGLP VMTSNVSTSV LGNCTVRQAR
TMQKFELSPF FMVDLVHHDG TVHPAINSLL RQFKLKESDT KLSTLAIPNA VTTFWKSARE
YNSLGARTTI DDAAKIPFMI KDVPEHLQEK LWETIQQYKG DAGFGRCTSA NACKIAYTLS
VSPFMIPATI NKIDALMAEE RQKLEYFQTV TANTCTISNF SISSLGDMIR SRYSTNHSRE
NLQKLQTVRD TIINFECQAG TSDGGTFDME TAQKLAEEYG CIDVIYHQSK GALSKRLGLK
GRWNQSLICK DLLIFCGVAI GGTWMMFQSF KDGMADVIRH QGKGKRQRQK LRYRQARDNK
MGIEVYGDDA TMEHYFGAAY TEKGKKSGKT KGMGTKNRRF VNMYGYNPED YSFIRFLDPL
TGKTMDEQVF TDISLVQDAF GKERLKLLSE GEIESEHMRN GIRAYLVKNL TTAALEIDMT
PHNSCQLGTK TNNIAGFVDR EYELRQTGEA RVVAPALIPK DNPITDEDIP VKHESKTLFR
GLRDYNPIAS AICLLTNESD GMKETMYGIG FGNTIITNQH LFRRNNGVLR VQSRHGEYVL
PNTTQLKVLP CEGRDIMVII LTPDFPPFPQ KLKFRPPIKG EKICLVGSLF QDKSITSTVS
ETSVTTPVDN SFLWKHWITT KDGHCGLPLV SSNDGYIVGI HSATSSRQTQ NYHAAMPEDF
HQTHLIDPVS KSWVKHWKYN PDNMVWGGIN LINSTPREPF KINKLVTDLF GDAVQFQSKQ
DEWFASQLKG NLKAVGKSTS QLVTKHTVKG KCMMFELYLQ THEEEKEFFK PLMGAYQKSR
LNREAFTKDI MKYSTPITVG IVDCDTFLKA EKGVIKRLEK LGFSGCEYVT DEEAIFQALN
MKAAVGALYS GKKRDYFESY GPEEKENILR ESCKRLYTGK FGVWNGSLKS ELRPMEKVMA
NKTRVFTAAP LDTLLAGKVC VDDFNNYFYS KNIEAPWTVG MTKFYGGWNE LLTKLPDGWV
YCDADGSQFD SSLSPFLINS VLRIRLKFME DWDLGEQMLK NLYTEIVYTA ILTPDSTIVK
KFKGNNSGQP STVVDNTLMV VLAMTYTLHK LGFEDEEQDS MCKYFVNGDD LIIAIKPEYE
SLLDQFQHCF KSLGLNYDFN SRTRKREELW FMSHCGIKKD GIFIPKLEPE RIVSILEWDR
SDQPVHRLEA ICAAMIESWG YDKLTHEIRK FYKWCLDEAP YADLAKAGKA PYIAECALKR
LYTSKEASEA ELEKYMEAIR SLVNDEDDDD MDEVYHQVDT KLDAGQGSKN DDKQKSSADS
KDNVITEKGS GSGQVRKDDD INAGLHGKHT IPRTKAITQK MKLPMIRGKV ALNLDHLLEY
EPNQRDISNT RATQKQYESW YDGVKNDYDV DDNGMQLILN GLMVWCIENG TSPNINGTWV
MMDSEEQVEY ALKPIIEHAK PTFRQIMAHF SDAAEAYIEM RNKKKPYMPR YGRLRGLNDM
GLARYAFDFY ETTSATPNRA REAHNQMKAA ALVGTQNRLF GMDGGGSTQE ENTERHTAAD
VNQNMHTLLG VRGLH


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