Reviewed, UniProtKB/Swiss-Prot P29152 (POLG_PSBMV)

Names and origin

Protein names	Recommended name:     Genome polyprotein Cleaved into the following 10 chains:     1- Recommended name:             P1 proteinase         Alternative name(s):             N-terminal protein     2- Recommended name:             Helper component proteinase                 Short name=HC-pro               EC=3.4.22.45     3- Recommended name:             Protein P3     4- Recommended name:             6 kDa protein 1                 Short name=6K1     5- Recommended name:             Cytoplasmic inclusion protein                 Short name=CI               EC=3.6.1.-     6- Recommended name:             6 kDa protein 2                 Short name=6K2     7- Recommended name:             Viral genome-linked protein         Alternative name(s):             VPg     8- Recommended name:             Nuclear inclusion protein A                 Short name=NI-a                 Short name=NIa               EC=3.4.22.44         Alternative name(s):             NIa-pro             49 kDa proteinase               Short name=49 kDa-Pro     9- Recommended name:             Nuclear inclusion protein B                 Short name=NI-b                 Short name=NIb               EC=2.7.7.48         Alternative name(s):             RNA-directed RNA polymerase     10- Recommended name:             Coat protein                 Short name=CP
Organism	Pea seed-borne mosaic virus (strain DPD1) [Complete proteome]
Taxonomic identifier	31736 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Pisum sativum (Garden pea) [TaxID: 3888]

Protein attributes

Sequence length	3206 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	Coat 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	Coat 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	Capsid protein Virion
Ligand	ATP-binding Nucleotide-binding
Molecular function	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: InterPro transcription, RNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW 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: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 397	397	P1 proteinase Potential		PRO_0000040375
	Chain	398 – 856	459	Helper component proteinase Potential		PRO_0000040376
	Chain	857 – 1214	358	Protein P3 By similarity		PRO_0000040377
	Chain	1215 – 1266	52	6 kDa protein 1 By similarity		PRO_0000040378
	Chain	1267 – 1902	636	Cytoplasmic inclusion protein By similarity		PRO_0000040379
	Chain	1903 – 1955	53	6 kDa protein 2 By similarity		PRO_0000040380
	Chain	1956 – 2149	194	Viral genome-linked protein By similarity		PRO_0000040381
	Chain	2150 – 2395	246	Nuclear inclusion protein A By similarity		PRO_0000040382
	Chain	2396 – 2915	520	Nuclear inclusion protein B By similarity		PRO_0000040383
	Chain	2916 – 3206	291	Coat protein By similarity		PRO_0000040384
Regions
	Domain	1338 – 1490	153	Helicase ATP-binding
	Domain	1494 – 1668	175	Helicase C-terminal
	Domain	2637 – 2761	125	RdRp catalytic
	Nucleotide binding	1351 – 1358	8	ATP Potential
	Motif	450 – 453	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	708 – 710	3	Involved in virions binding and aphid transmission By similarity
	Motif	1440 – 1443	4	DECH box
	Motif	1994 – 2001	8	Nuclear localization signal Potential
Sites
	Active site	348	1	For P1 proteinase activity By similarity
	Active site	742	1	For helper component proteinase activity By similarity
	Active site	815	1	For helper component proteinase activity By similarity
	Active site	2195	1	For nuclear inclusion protein A activity By similarity
	Active site	2230	1	For nuclear inclusion protein A activity By similarity
	Active site	2300	1	For nuclear inclusion protein A activity By similarity
	Site	397 – 398	2	Cleavage; by P1 proteinase Potential
	Site	856 – 857	2	Cleavage; by HC-pro Potential
	Site	1214 – 1215	2	Cleavage; by NIa-pro By similarity
	Site	1266 – 1267	2	Cleavage; by NIa-pro By similarity
	Site	1902 – 1903	2	Cleavage; by NIa-pro By similarity
	Site	1955 – 1956	2	Cleavage; by NIa-pro By similarity
	Site	2149 – 2150	2	Cleavage; by NIa-pro By similarity
	Site	2395 – 2396	2	Cleavage; by NIa-pro By similarity
	Site	2915 – 2916	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	2016	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	P29152-1 [UniParc]. Last modified December 1, 1992. Version 1. Checksum: 42A3D921BE9A0CBF	FASTA	3,206	364,276
	10 20 30 40 50 60 MSTLVCQAVA APVWSNGART RRIRDADGEY RCTQCDMGFD SMTMARPVNH CCDGIMIDEY 70 80 90 100 110 120 NLYDDDPIMH LVDSKTPIKR GSQETEGDGM AAEAIKVTGA EPVNCFMVGT IKCKINENSI 130 140 150 160 170 180 VAKGVMAAIP RQLTQDEVFM RKARLQAAVA KSTIEREEKE RQFAFSKLEE KLRARREKLK 190 200 210 220 230 240 DGIVIKTRKG LEWREATPNQ QRGKLQSTSF DASGGKTLTP HTIYCKTKSS KFSNGGVKCA 250 260 270 280 290 300 TSKKMRTVRK PQSLKMKTES IDVLIEQVMT IAGKHAKQVT LIDKQKTNRV WIRRVNGVRL 310 320 330 340 350 360 LQVETKHHKG IISQKDASLN NLTKRVARHF ARKTAYIHPS DSITHGHSGV VFLRANISGS 370 380 390 400 410 420 KSYSIDDLFV VRGKRNGKLM ESRNKVAWRK MFQIDHFSIV GIKIWNAFDA EYVKLRDESV 430 440 450 460 470 480 SDHDCVGGIT PEECGILAAQ ILRVFYPCWR ITCTKCISNW LSKPTSEQIE HIYERGNLAI 490 500 510 520 530 540 QDLNKRIPSA HHVTQMVELL RQRIKNTTFD MGNNTKVHEL IGHRQDGVFR HLNRLNNSIL 550 560 570 580 590 600 AANGSSTIEW ESMNESLLEL ARWHNKRTES IASGGISSFR NKISAKAQIN FALMCDNQLD 610 620 630 640 650 660 TNGNFVWGER GYHAKRFFSE FFTKIDPKDG YSHHTVRATP TGVRHLAIGN LIIPGDLQKL 670 680 690 700 710 720 REKLEGVSIT AVGISEKCVS RRNGDFVYPC SCVTSENGKP VLSDVILPTR NHLVIGNTGD 730 740 750 760 770 780 PKLVDLPKTE TGRMWIAKEG YCYINIFFAM LVNVSEKDAK DFTKFVRDEI MPQLGKWPTM 790 800 810 820 830 840 MDVATACYKL AIIYPDVRDA QLPRILVDHS EQIFHVIDSY GSMTTGYHIL KAGTVSQLIS 850 860 870 880 890 900 FAHGALLGEM KMYRVGGTQK MEINMCCCQR KNLLIKQLIR AIYRPKLLTE IIETEPFVLM 910 920 930 940 950 960 LAIVSPSILK AMFRSGTFNQ AIKFYMHRSK PTAQTLAFLE ALSERVSRSR VLSEQFNIID 970 980 990 1000 1010 1020 GALKELKSLA NMSMRTQHTY PIVQNQLDIM IERVSADAEL LRDGFVVSKG RVQALIEKNY 1030 1040 1050 1060 1070 1080 QDDLRNSFTD LPYVQQLQQT MSFSRVKHGF GELCESKDLS FSKEAWMGHL SSFSAGGKQI 1090 1100 1110 1120 1130 1140 IRLARTKSQQ MLASGGRRVT LAARNITMRM VTATFSEIMK FVNMLLVLSM IFKLWKQANT 1150 1160 1170 1180 1190 1200 LLEEREKDKW EKFDRSQNEL RRQLRYTLWR FEAQEGRQVT REEFFDYLKY NEGIENRHEL 1210 1220 1230 1240 1250 1260 INELIANQPL FSIQAKKHGE IRFEQTVALM ALLAMMFGSD RSDAVFSTLS KVRTIFTTMA 1270 1280 1290 1300 1310 1320 QEVRCQSIDD IHDVFDEKKA TIDFELATDQ PAQVQMDKTF CEWWQNQMEQ NRTVPHYRTG 1330 1340 1350 1360 1370 1380 GKFIEFTRSN AASVANEIAH TPDFSEYLIR GAVGSGKSTG LPCYLSAKGR VLLLEPTRPL 1390 1400 1410 1420 1430 1440 TENVCAQLRG SPFHKSPSMS MRNGHTFGST PIHVMTTGYA LHFFCNNVER IREYDFVIFD 1450 1460 1470 1480 1490 1500 ECHVIDSSAM SFYCALKEYS YQGKILKVSA TPPGREVEFK TQFPVTIATE DSLSFDQFVQ 1510 1520 1530 1540 1550 1560 AQGSGANCDI LKKGHNILVY VSSYNEVDRL SKLLVDRGFK VTKVDGRTMK LGGVEINTSG 1570 1580 1590 1600 1610 1620 TAEKPHFIVA TNIIENGVTL DIDVVVDFGV KVVAELDADA RTMRYNKQAI SYGERIQRLG 1630 1640 1650 1660 1670 1680 RVGRLKDGHA LRIGHTEKGI TEIPVAIAVE SAFQCFAYGL PVMTSNVSTS IIGNCTVKQA 1690 1700 1710 1720 1730 1740 RTMMNFELSP FFTVELVKYN GTMHPEIHKI LVPYKLRDSS MQLCKEAIPN SGVSRWHTAH 1750 1760 1770 1780 1790 1800 EYISHGIVLE TLKSDVRIPF YLKGVPEKVY EKIWNAVCVF KSDSGFGRMS TASACNVAYT 1810 1820 1830 1840 1850 1860 LKTDPLSITR TIAHIDALLI EEQEKKSQFD LMSSHVTNSS SISLAGLVNR LRSKWMVDHS 1870 1880 1890 1900 1910 1920 GENIVKLQNA RSQLLEFRGM DINLDDVESF RKFGCAETVR CQSKSEVSKT LQLKGKWNKP 1930 1940 1950 1960 1970 1980 LITSDFFVVC MVSIGCVVLM YQIFMAKWNE PVKLEGKSKA KTLRFRQARD NNAKYEVFAD 1990 2000 2010 2020 2030 2040 EDTKRHYFGE AYTKKGKKSG KARGMGVKTK KFVNVYGFDP CEYSLVRFVD PLTGLTYDRH 2050 2060 2070 2080 2090 2100 PMEHMMDVQE TIGDDRREAM WNDELDKQLF VTRPTIEAYY IKDKTTPALK IDLNPHNPMR 2110 2120 2130 2140 2150 2160 VCDKAETIAG FPEREFELRQ SGSATLVPYS EVPVQNEKQE FDEEHVRTEA ASLHFGLRDY 2170 2180 2190 2200 2210 2220 NPIAQAVCRI TNTGVDYDRS IFGIGFGQFL ITNAHCFKLN EGETRIVSRH GQFTIEKTHS 2230 2240 2250 2260 2270 2280 LPIHQVKDKD MVIVRLPKDF PPFPQRLQFR APQEREKICL VGSNFQEKSI QSVITESCMT 2290 2300 2310 2320 2330 2340 FKHNGGKYWK HWITTKEGHC GLPAVALKDG HIVGIHNLGG ENTNINYFTP FDADILDKYL 2350 2360 2370 2380 2390 2400 LNAEALQWTK GWKYNKNKVC WGGLELLDDN EPEESGLFRM VKLLKSLEED GVRTQSRDDA 2410 2420 2430 2440 2450 2460 WLEKEIKGSL KVVARCPGQL VTKHVVKGPC AMFQLYLELH EDAKSFFTPR MGSYGKSRLS 2470 2480 2490 2500 2510 2520 KGAFIKDIMK YSSNTVVGNV DCDVFENAID NVEKILWKAG MMQCEYVTDA EAIFQSLNMN 2530 2540 2550 2560 2570 2580 AAVGAMYQGK KKDYFEDFTA ADRELIVKQS CERLFLGKKG VWNGSLKAEL RPIEKVHENK 2590 2600 2610 2620 2630 2640 TRTFTAAPLD TLLGGKVCVD DFNNFFYSCH LRGPWTVGIT KFYAGWNEFL SKLPDGWLYC 2650 2660 2670 2680 2690 2700 DADGSRFDSS LTPYLINAVL ELRLRFMEEW DAGEQMLKNL YTEIIYTPIA TPDGSVIKKT 2710 2720 2730 2740 2750 2760 KGNNSGQPST VVDNTLMVIL AMQYSLQLLG VDFETQDEVV RYFANGDDLL IAVRPDCEFV 2770 2780 2790 2800 2810 2820 LKGLEIHFSN LGLNYNFSAR HHDKKDVWFM STRGILRDGI LIPKLEEERI VAILEWDRSR 2830 2840 2850 2860 2870 2880 EFSHRLDAIC AAMIEAWGYD ELLQHIRKFY YWLLEQEPYR SIAQEGKAPY IAETALRHLY 2890 2900 2910 2920 2930 2940 TNAMATQSEL EKYTEAINQH YNDEGGDGSI KVRLQAGDET KDDERRRKEE EDRKKREESI 2950 2960 2970 2980 2990 3000 DASQFGSNRD NKKNKNKESD TPNKLIVKSD RDVDAGSSGT ITVPRLEKIS AKIRMPKHKG 3010 3020 3030 3040 3050 3060 GVAISLQHLV DYNPAQVDIS NTRATQSQFD NWWRAVSQEY GVGDNEMQVL ASGLMVWCIE 3070 3080 3090 3100 3110 3120 NGTSPNINGM WTMMDGEEQV EYPLKPVMDN ARPTFRQIMA HFSDVAEAYI EKRNSTEVYI 3130 3140 3150 3160 3170 3180 PRYALQRNLR DPSLARYGFD FYEITAKTPV RAREAHFQMK AAAIRGKSNS LFGLDGNVGT 3190 3200 QEENTERHTA EDVNQNMHNL LGMRAM

References

[1]	"The complete nucleotide sequence of pea seed-borne mosaic virus RNA." Johansen E., Rasmussen O.F., Heide M., Borkhardt B. J. Gen. Virol. 72:2625-2632(1991) [PubMed: 1940858] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"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
EMBLGenBankDDBJ	D10930 mRNA. Translation: BAA01726.1.
PIR	GNVSPV. JQ1331.
RefSeq	NP_056765.1.
3D structure databases
HSSP	HSSP built from PDB template 1LVM based on UniProtKB P04517.
ModBase	Search...
Protein family/group databases
MEROPS	C04.010. C06.001.
Genome annotation databases
GeneID	1494045.
Family and domain databases
InterPro	IPR014001. DEAD-like_N. IPR001650. DNA/RNA_helicase_C. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR014021. Helicase_SF1/SF2_ATP-bd. IPR002540. Pept_S30_P1_potyvir. IPR001730. Peptidase_C4. IPR001456. Peptidase_C6. IPR001592. Poty_coat. IPR013648. PP_Potyviridae. IPR001205. RNA_pol_P3D. IPR007094. RNA_pol_PSvir. [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]
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_PSBMV

Accession

Primary (citable) accession number: P29152

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	December 1, 1992
Last modified:	June 16, 2009
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)