P31999 (POLG_LMVE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 10 chains: P1 proteinase EC=3.4.-.- Alternative name(s): N-terminal protein Helper component proteinase Short name=HC-pro EC=3.4.22.45 Protein P3 6 kDa protein 1 Short name=6K1 Cytoplasmic inclusion protein Short name=CI EC=3.6.4.- 6 kDa protein 2 Short name=6K2 Viral genome-linked protein Alternative name(s): VPg Nuclear inclusion protein A Short name=NI-a Short name=NIa EC=3.4.22.44 Alternative name(s): 49 kDa proteinase Short name=49 kDa-Pro NIa-pro Nuclear inclusion protein B Short name=NI-b Short name=NIb EC=2.7.7.48 Alternative name(s): RNA-directed RNA polymerase Capsid protein Short name=CP Alternative name(s): Coat protein
Organism	Lettuce mosaic virus (strain E) (LMV) [Complete proteome]
Taxonomic identifier	117131 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Spinacia oleracea (Spinach) [TaxID: 3562] Cicer arietinum (Chickpea) (Garbanzo) [TaxID: 3827] Pisum sativum (Garden pea) [TaxID: 3888] Carthamus tinctorius (Safflower) [TaxID: 4222] Lactuca [TaxID: 4235] Cichorium intybus (Chicory) [TaxID: 13427] Eustoma grandiflorum (Bluebells) (Lisianthus russellianus) [TaxID: 52518] Cichorium endivia (Endive) [TaxID: 114280]

Protein attributes

Sequence length	3255 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Capsid protein is 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 is a RNA-dependent RNA polymerase that plays an essential role in the virus replication. Helper component proteinase is required for aphid transmission and also has proteolytic activity. 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. Both 6K peptides are indispensable for virus replication By similarity. 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. 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.
Subcellular location	Capsid protein: Virion Potential.
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.
Post-translational modification	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. The viral RNA of potyviruses is expressed as a single polyprotein which 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.
Sequence similarities	Belongs to the potyviruses polyprotein family. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 peptidase C4 domain. Contains 1 peptidase C6 domain. Contains 1 peptidase S30 domain. Contains 1 RdRp catalytic domain.

Ontologies

Keywords
Biological process	RNA replication
Cellular component	Virion
Ligand	ATP-binding Nucleotide-binding
Molecular function	Capsid protein Helicase Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Suppressor of RNA silencing Thiol protease Transferase
PTM	Covalent protein-RNA linkage Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular component	viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 437	437	P1 proteinase Potential		PRO_0000040269
	Chain	438 – 895	458	Helper component proteinase Potential		PRO_0000040270
	Chain	896 – 1273	378	Protein P3 By similarity		PRO_0000040271
	Chain	1274 – 1325	52	6 kDa protein 1 By similarity		PRO_0000040272
	Chain	1326 – 1968	643	Cytoplasmic inclusion protein By similarity		PRO_0000040273
	Chain	1969 – 2021	53	6 kDa protein 2 By similarity		PRO_0000040274
	Chain	2022 – 2214	193	Viral genome-linked protein By similarity		PRO_0000040275
	Chain	2215 – 2457	243	Nuclear inclusion protein A By similarity		PRO_0000040276
	Chain	2458 – 2977	520	Nuclear inclusion protein B By similarity		PRO_0000040277
	Chain	2978 – 3255	278	Capsid protein By similarity		PRO_0000040278
Regions
	Domain	1397 – 1549	153	Helicase ATP-binding
	Domain	1568 – 1727	160	Helicase C-terminal
	Domain	2215 – 2433	219	Peptidase C4
	Domain	2699 – 2823	125	RdRp catalytic
	Nucleotide binding	1410 – 1417	8	ATP Potential
	Motif	489 – 492	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	747 – 749	3	Involved in virions binding and aphid transmission By similarity
	Motif	1499 – 1502	4	DECH box
	Motif	2062 – 2069	8	Nuclear localization signal Potential
	Compositional bias	1266 – 1271	6	Poly-Glu
	Compositional bias	2965 – 2972	8	Poly-Asp
Sites
	Active site	345	1	For P1 proteinase activity By similarity
	Active site	354	1	For P1 proteinase activity Potential
	Active site	388	1	For P1 proteinase activity By similarity
	Active site	781	1	For helper component proteinase activity By similarity
	Active site	854	1	For helper component proteinase activity By similarity
	Active site	2260	1	For nuclear inclusion protein A activity By similarity
	Active site	2295	1	For nuclear inclusion protein A activity By similarity
	Active site	2365	1	For nuclear inclusion protein A activity By similarity
	Site	437 – 438	2	Cleavage; by P1 proteinase Potential
	Site	895 – 896	2	Cleavage; by HC-pro Potential
	Site	1273 – 1274	2	Cleavage; by NIa-pro By similarity
	Site	1325 – 1326	2	Cleavage; by NIa-pro By similarity
	Site	1968 – 1969	2	Cleavage; by NIa-pro By similarity
	Site	2021 – 2022	2	Cleavage; by NIa-pro By similarity
	Site	2214 – 2215	2	Cleavage; by NIa-pro By similarity
	Site	2457 – 2458	2	Cleavage; by NIa-pro By similarity
	Site	2977 – 2978	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	2084	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	P31999 [UniParc]. Last modified June 6, 2002. Version 3. Checksum: 763F676F95876A12	FASTA	3,255	367,571
	10 20 30 40 50 60 MATLDNCTQV HHMFAYNREH GTNYTRNHFR RYLAAQRIGF YYDWDDDVYE CPTCEAIYHS 70 80 90 100 110 120 LDDIKNWHEC DPPAFDLNDF ITDARLKSAP VPDLGPVIIE IPKAEEKQEL NFFAATPAPE 130 140 150 160 170 180 VSQWKCRGLQ FGSFTELETS EPVASAPEPK CEEPARTIAK PEESVEQETR GDGKRLLQAQ 190 200 210 220 230 240 MEVDKAEQDL AFACLNASLK PRLEGRTTAT IARRRDGCLV YKTKPSWSQR RRAKKTLKVD 250 260 270 280 290 300 TLACENPYIP AIVDKISIAG GSSASVMHEQ QKPKTLHTTP SRKVATHYKR TVMNQQTLMA 310 320 330 340 350 360 FINQVGTILL NAEKEFEVVG CRKQKVTGKG TRHNGVRLVK LKTAHEEGHR RRVDIRIPNG 370 380 390 400 410 420 LRPIVMRISA RGGWHRTWTD SELSPGSSGY VLNSSKIIGK FGLRRHSIFV VRGRVDGEVI 430 440 450 460 470 480 DSQSKVTHSI THRMVQYSDV ARNFWNGYST CFMHNTPKDI LHTCTSDFDV KECGTVAALL 490 500 510 520 530 540 TQTLFQFGKI TCEKCAIEYK NLTRDELATR VNKEIDGTII SIQTQHPRFV HVLNFLRLIK 550 560 570 580 590 600 QVLNAKNGNF GAFQETERII GDRMDAPFSH VNKLNAIVIK GNQATSDEMA QASNHVLEIA 610 620 630 640 650 660 RYLKNRTENI QKGSLKSFRN KISGKAHLNP SLMCDNQLDK NGGFEWGQRS YHAKRFFDGY 670 680 690 700 710 720 FETIDPSDGY SKYTIRRNPN GHRKLAIGNL IVSTNFESHR RSMIGESIED PGLTNQCVSK 730 740 750 760 770 780 EGDTFIYPCC CVTDEYGKPT LSEIKMPTKH HLVLGNAGDP KYVDLPKEAE GKMFVTKDGY 790 800 810 820 830 840 CYINIFLAML VDVPEDQAKD FTKMAREIAV KQLGEWPSMM DVATACNILA TFHPDTRRSE 850 860 870 880 890 900 LPRILVDHAT KTFHVIDSYG SITTGFHILK ANTVTQLVKF AHESLESEMQ HYRVGGEPDK 910 920 930 940 950 960 APRKPAGSVP TLGISDLRDL GVELENEEHS IRPNLQRLIK AIYRPRMMRS LLTEEPYLLI 970 980 990 1000 1010 1020 LSIVSPGVLM ALYNSGSLER TMHEFLQTDQ RLSATAQILK HLAKKVSLAK TLTIQNAILE 1030 1040 1050 1060 1070 1080 GGAGSLNEIL DAPAGRSLSY RLAKQTVEVM MARSDMDKEL VDVGFSVLRD QKNELIEKSY 1090 1100 1110 1120 1130 1140 LMDLEDSWHA LPLCGKLSAM RASRRWRDTS TPEVIPTGAA DLKGRYSISV GSVSKSAILH 1150 1160 1170 1180 1190 1200 LKGICSGAVK RVRDKWVGVQ VQGVKWLAKS VHYMIPELTN ILNVGTLLLT LISLGVAFRN 1210 1220 1230 1240 1250 1260 LTGQFKEMKH KETLAKEEEL RKRIRTYNST YYEIHGKHAD AKQITKFITH HDPKLLEVVE 1270 1280 1290 1300 1310 1320 FYEGPEEEEV EHQAKREDQA NLERIIAFTA LVMMMFDSER SDCVYRSLSK LKSLVSTCED 1330 1340 1350 1360 1370 1380 DVRHQSVDEI IDLFDEKKET IDFEIEGKEL YSSRVVDSTF SKWWDNQLVR GNTMAHYRTE 1390 1400 1410 1420 1430 1440 GHFMTFTRET AASVAAEIAH NEYRDILLQG GVGSGKSTGL PFHLHRKGGV LLIEPTRPLA 1450 1460 1470 1480 1490 1500 QNVYKQLGSS PFHLSPNLRM RGSCKFGSSQ VTVATSGYAL HFIANNAQSL KAYDFIIFDE 1510 1520 1530 1540 1550 1560 CHVLDASAMA FRCLLQEFEY QGKIIKVSAT PPGRKLDFKP MHMVDIATEN ELSIQQFVQG 1570 1580 1590 1600 1610 1620 QGTGVNCDAT KKGDNILVYV SSYNEVDMLS KMLNDKGYKV TKVDGRTMKL GSVEVETVGT 1630 1640 1650 1660 1670 1680 PQRKHFVVAT NIIENGVTLD VDVVVDFGQK VVPILDSEHR MIRYTKKSIT YGERIQRVGR 1690 1700 1710 1720 1730 1740 VGRNKAGSAI RIGSTEMGTE EIPASIATEA AFLCFTYGLP VMTSNVSTSV LGNCTVRQAR 1750 1760 1770 1780 1790 1800 TMQKFELSPF FMVDLVHHDG TIHPAINSLL KQFKLKESDI KLSTLAIPNA VTTFWKSARE 1810 1820 1830 1840 1850 1860 YNSLGARTTI DDAAKIPFMI KDVPEHLQEK LWETIQQYKG DAGFGRCTSA NACKIAYTLS 1870 1880 1890 1900 1910 1920 VSPFMIPATI NKIDALMAEE RQKMEYFQTV TANTCTISNF SISSIGDMIR SRYSTNHSRE 1930 1940 1950 1960 1970 1980 NLQKLQAVRD TIINFECQAG TGDGGSFDME TAQKLAEEYG CIDVIYHQSK EALSKRLGLK 1990 2000 2010 2020 2030 2040 GRWNQSLICK DLLVFCGVAI GGTWMMFQSF KDGMADAVRH QGKGKRQRQK LRYRQARDNK 2050 2060 2070 2080 2090 2100 VGIEVYGDDA TMEHYFGAAY TEKGKKSGKT KGMGTKNRRF VNMYGYNPED FSFIRFLDPL 2110 2120 2130 2140 2150 2160 TGKTMDEQVF SDISLVQDAF SKERLKLLSE GEIESEHMRN GIRAYLVKNL TTAALEIDMT 2170 2180 2190 2200 2210 2220 PHNSCQLGAK TNNIAGYVDR EYELRQTGEA RVVAPALIPK DNPITDEDIP VKHESKTLFR 2230 2240 2250 2260 2270 2280 GLRDYNPIAA AICLLTNESD GMKETMYGIG FGNTIITNQH LFRRNNGVLR VQSRHGEYVL 2290 2300 2310 2320 2330 2340 PNTTQLKVLP CEGRDIMVII LTPDFPPFPQ KLKFRPPIKG EKICLVGSLF QDKSITSTVS 2350 2360 2370 2380 2390 2400 ETSVTTPVDN SFLWKHWITT KDGHCGLPLV SSNDGYIVGI HSATSSRQTQ NYHAAMPEDF 2410 2420 2430 2440 2450 2460 HQTHLIDPAS KSWVKHWKYN PDNMVWGGIN LINSTPREPF KINKLVTDLF GDAVQFQSKQ 2470 2480 2490 2500 2510 2520 DEWFASQLKG NLKAVGKSTS QLVTKHTVKG KCMMFELYLQ THEEEKEFFK PLMGAYQKSR 2530 2540 2550 2560 2570 2580 LNREAFTKDI MKYSTPITVG IVDCDTFLKA EEGVIKRLER LGFSGCEYVT DEEAIFQALN 2590 2600 2610 2620 2630 2640 MKAAVGALYS GKKRDYFEGY GPEEKENILR ESCKRLYTGK FGVWNGSLKS ELRPMEKVMA 2650 2660 2670 2680 2690 2700 NKTRVFTAAP LDTLLAGKVC VDDFNNYFYS KNIEAPWTVG MTKFYGGWNE LLTKLPDGWV 2710 2720 2730 2740 2750 2760 YCDADGSQFD SSLSPFLINS VLRIRLKFME DWDLGEQMLK NLYTEIVYTA ILTPDSTIVK 2770 2780 2790 2800 2810 2820 KFKGNNSGQP STVVDNTLMV VLAMTYTLHK LGFEDEEQDS MCKYFVNGDD LIIAIKPEHE 2830 2840 2850 2860 2870 2880 SLLDQFQHCF KSLGLNYDFN SRTRKKEELW FMSHCGIKKD GIFIPKLEPE RIVSILEWDR 2890 2900 2910 2920 2930 2940 SDQPVHRLEA ICAAMIESWG YDKLTHEIRK FYKWCLEQAP YADLAKAGKA PYIAECALKR 2950 2960 2970 2980 2990 3000 LYTSKEASEA ELEKYMEAIR SLVNDEDDDD MDEVYHQVDA KLDAGQGSKT DDKQKNSADP 3010 3020 3030 3040 3050 3060 KDNIITEKGS GSGQMKKDDD INAGLHGKHT IPRTKAITQK MKLPMIRGKV ALNLDHLLEY 3070 3080 3090 3100 3110 3120 EPNQRDISNT RATQKQYESW YDGVKNDYDV DDSGMQLILN GLMVWCIENG TSPNINGTWV 3130 3140 3150 3160 3170 3180 MMDGEEQVEY ALKPIIEHAK PTFRQIMAHF SDAAEAYIEM RNKKKPYMPR YGRLRGLNDM 3190 3200 3210 3220 3230 3240 GLARYAFDFY ETTSATPNRA REAHNQMKAA ALVGTQNRLF GMDGGGSTQE ENTERHTAAD 3250 VNQNMHTLLG VRGLH

References

[1]	"Comparison of the complete nucleotide sequences of two isolates of lettuce mosaic virus differing in their biological properties." Revers F., Yang S.J., Walter J., Souche S., Lot H., Le Gall O., Candresse T., Dunez J. Virus Res. 47:167-177(1997) [PubMed: 9085548] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	Le Gall O. Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO 1750 AND 1771.
[3]	"Nucleotide sequence of the 3' terminal region of lettuce mosaic potyvirus RNA shows a Gln/Val dipeptide at the cleavage site between the polymerase and the Capsid protein." Dinant S., Lot H., Albouy J., Kuziak C., Meyer M., Astier-Manifacier S. Arch. Virol. 116:235-252(1991) [PubMed: 2001176] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2776-3255.
[4]	"Potyvirus proteins: a wealth of functions." Urcuqui-Inchima S., Haenni A.L., Bernardi F. Virus Res. 74:157-175(2001) [PubMed: 11226583] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X97704 mRNA. Translation: CAA66280.2. X65652 Genomic RNA. Translation: CAA46602.1.
PIR	S70859.
3D structure databases
ProteinModelPortal	P31999.
SMR	P31999. Positions 2223-2436.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR014001. DEAD-like_helicase. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR001650. Helicase_C. IPR009003. Pept_cys/ser_Trypsin-like. IPR002540. Pept_S30_P1_potyvir. IPR001730. Peptidase_C4. IPR001456. Peptidase_C6. IPR001592. Poty_coat. IPR013648. PP_Potyviridae. IPR001205. RNA-dir_pol_picornavirus. IPR007094. RNA-dir_pol_PSvirus. [Graphical view]
Pfam	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]
PRINTS	PR00966. NIAPOTYPTASE.
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	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]
ProtoNet	Search...

Entry information

Entry name

POLG_LMVE

Accession

Primary (citable) accession number: P31999
Secondary accession number(s): P90263

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	June 6, 2002
Last modified:	November 16, 2011
This is version 103 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program