Reviewed, UniProtKB/Swiss-Prot O56075 (POLG_PEMVM)

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	Peanut mottle virus (strain M) [Complete proteome]
Taxonomic identifier	103926 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Arachis hypogaea (Peanut) [TaxID: 3818] Glycine max (Soybean) [TaxID: 3847] Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885] Pisum sativum (Garden pea) [TaxID: 3888] Stylosanthes [TaxID: 35627] Cassia [TaxID: 53851] Arachis pintoi [TaxID: 108216]

Protein attributes

Sequence length	3099 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology.

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: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 322	322	P1 proteinase Potential		PRO_0000040305
	Chain	323 – 779	457	Helper component proteinase Potential		PRO_0000040306
	Chain	780 – 1128	349	Protein P3 By similarity		PRO_0000040307
	Chain	1129 – 1180	52	6 kDa protein 1 By similarity		PRO_0000040308
	Chain	1181 – 1814	634	Cytoplasmic inclusion protein By similarity		PRO_0000040309
	Chain	1815 – 1867	53	6 kDa protein 2 By similarity		PRO_0000040310
	Chain	1868 – 2057	190	Viral genome-linked protein By similarity		PRO_0000040311
	Chain	2058 – 2303	246	Nuclear inclusion protein A By similarity		PRO_0000040312
	Chain	2304 – 2821	518	Nuclear inclusion protein B By similarity		PRO_0000040313
	Chain	2822 – 3099	278	Coat protein By similarity		PRO_0000040314
Regions
	Domain	1252 – 1404	153	Helicase ATP-binding
	Domain	1423 – 1582	160	Helicase C-terminal
	Domain	2545 – 2669	125	RdRp catalytic
	Nucleotide binding	1265 – 1272	8	ATP Potential
	Motif	374 – 377	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	631 – 633	3	Involved in virions binding and aphid transmission By similarity
	Motif	1354 – 1357	4	DESH box
	Motif	1906 – 1915	10	Nuclear localization signal Potential
Sites
	Active site	665	1	For helper component proteinase activity By similarity
	Active site	738	1	For helper component proteinase activity By similarity
	Active site	2103	1	For nuclear inclusion protein A activity By similarity
	Active site	2138	1	For nuclear inclusion protein A activity By similarity
	Active site	2208	1	For nuclear inclusion protein A activity By similarity
	Site	322 – 323	2	Cleavage; by P1 proteinase Potential
	Site	779 – 780	2	Cleavage; by HC-pro Potential
	Site	1128 – 1129	2	Cleavage; by NIa-pro By similarity
	Site	1180 – 1181	2	Cleavage; by NIa-pro By similarity
	Site	1814 – 1815	2	Cleavage; by NIa-pro By similarity
	Site	1867 – 1868	2	Cleavage; by NIa-pro By similarity
	Site	2057 – 2058	2	Cleavage; by NIa-pro By similarity
	Site	2303 – 2304	2	Cleavage; by NIa-pro By similarity
	Site	2821 – 2822	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1930	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	O56075-1 [UniParc]. Last modified June 1, 1998. Version 1. Checksum: 0D8E9FC7603F0A4B	FASTA	3,099	351,038
	10 20 30 40 50 60 MASITFGNAC TVVFGQVRKE EVTAGPVAVN LNEGTRMVVV PTAAQMATPT PSVSIKIINR 70 80 90 100 110 120 WSNKAVSSYE RQVEDVFANF FAKKERSDEL LTRYYGKVVQ KGNKLMVKRA PLHVARVLEK 130 140 150 160 170 180 QRLQDIEDEK AFLQYRDAGV HVAGSVKFTD TRSRGQTVSF RTEHYKPTGK IVQKKKAQKQ 190 200 210 220 230 240 RANADVDHLI DEVMKICSAD CKQVEFISMG KRRLTAKFKL FGKSVIPCIH LAHEQGRRLR 250 260 270 280 290 300 RELDPRIHEQ VIAHLVTGRK VRELIKDDMV TYGWSGAILN KNLFKRTPFR WDEVVIRGRL 310 320 330 340 350 360 YGKLVDARSK LSECSKDKIH QYSSFEAQFW KGWKNKFDTL HPHNKDHICE PTINNEKCGE 370 380 390 400 410 420 IVATIFQAIH PVIKVSCSTC RERLTKASNE ELNEYLATNL ACHKATFDDM RQQHATVNTV 430 440 450 460 470 480 LNKIEQTSLA NPNLKDSMEI VRLLQNLNQT QARQLMKVNN TLLKGNVATS EEFSDATTQL 490 500 510 520 530 540 LEVTRWYAKH LSLVDEGSIS SFRNKATSKS LINPSLLCDN QLDRNGNFVW GERGRHSKRF 550 560 570 580 590 600 FENFFEEVVP GGGYKKYQIR NSPNCTRKLA IGNLIVPMSL ERARNALIGE SVERLPVTEA 610 620 630 640 650 660 CVSRVNGAFM HVASCVTSDN GSAHFSPLYS PTKRHLVVGT TGDSKYIDLP ATESDKMYVA 670 680 690 700 710 720 KEGYCYINIF LAMLVNVNED SAKDFTKMIR DTIVPMLGTW PSMMDVATAC YILTVFHPET 730 740 750 760 770 780 KSAELPRILV DHTNKTMHVI DSFGSISTGY HILKAGTVSQ LIHFASNELV SEMKHYVVGG 790 800 810 820 830 840 EAPHARRMRM EKALIQGIFK PKQLVYLIEE DPYILMMSLV SPTLLINLFN VGGLEVAMKH 850 860 870 880 890 900 WIKKEMNIGL IFSMLSSLAQ KVSRADLVNE QITMIDANAA QFIETLAGID VENPMRNELV 910 920 930 940 950 960 SALTMMLARS DVDSTLNKTG FTGFSDTLLE MREKIIGDEL NKVWSELSWW EKFSSIIFSR 970 980 990 1000 1010 1020 RARKHIMAPL PNTKLHAIDD RYAISCTWLH GKIKARFNGA KSATLEVCKK VTSILKRNTV 1030 1040 1050 1060 1070 1080 DSILYICRKC YSDIFYFVNV MLISSMILSV IYTMHKMVIE SRAHKQAMVI MKMREDELVV 1090 1100 1110 1120 1130 1140 KQMYDQYCKL ANETPTKEEF FQYVCKMNKE LGERIAPEFE EGSLVVYQAK TETELGLEKV 1150 1160 1170 1180 1190 1200 VAYLALIAMI FDGERSDAVF RALSKLKTVF GTLGETVRYQ SLDEIESVAD EKKMTIDFEL 1210 1220 1230 1240 1250 1260 EGSEASSSTV MSAKFSDWWY KQLETNRVVP HYRIGGEFVE FTRKTAAEVV NNMRASNASE 1270 1280 1290 1300 1310 1320 FLVRGAVGSG KSTGLPHLLA QKGRVLLLEP TRPLAENVCK QLRQAPFQQN PTLRMRGLTT 1330 1340 1350 1360 1370 1380 FGSSNIVIMT SGFALHYYAN NPTKLQEYDF VMIDESHTMD ASAMAFYCLV REYNFQGKII 1390 1400 1410 1420 1430 1440 KVSATPPGKE CEFKTQFDVA LLIEEDLSFQ QFAQSQGQGG NADMTKHGDN ILVYVASYND 1450 1460 1470 1480 1490 1500 VDQLAELLIR GNHFVTKVDG RTMKMGSTEI VSKGTASKKH YIIATNIIEN GVTLDVDVVV 1510 1520 1530 1540 1550 1560 DFGQKVVAEL DGDSRCMRYR KVAVSYGERI QRLGRVGRVK KGTALRIGHT EHGISEIPAS 1570 1580 1590 1600 1610 1620 ISTEAAFLCF AYGLPVITHN VTVSILANCT VQQARTMMLF ELSPFFLADL VKYNGSMHPE 1630 1640 1650 1660 1670 1680 VHKLLKPYKL RDSEIELCKL AIPNSSIGRW LSVHEYAKLG IKIHAVDSVR IPFAGRGIPD 1690 1700 1710 1720 1730 1740 KLYSELWHII QEHKHEAGFG RLTSASASTI AYTLSTDPEA IPRTIALLDN LIAEEMQKKA 1750 1760 1770 1780 1790 1800 HFEALNSTLC SQRFTLKNIV DTVRQRYMKD HSKHNIEVLQ SARSQILEFN SATHDFKKVA 1810 1820 1830 1840 1850 1860 SLLGYGFLDT VQYQSKNELS KRLGLKGRWN KSLVTNDLLV CGMVLFGGVW MVWEYAKSAM 1870 1880 1890 1900 1910 1920 NEPVRYQGKR QNQKLKFRDA RDRKVGREVY GDDGTIEHFF GEAYTKKGKS KGNHTVKGMG 1930 1940 1950 1960 1970 1980 RKTRRFIHMY GFDPTEYSFV RFVDPLTGYA IDENITCDIS LVQDEVAEVR KQFINEDEIS 1990 2000 2010 2020 2030 2040 AQSIAENPGI IAYYMSRNAD KALKIDLTPH NPLAVGRGGS SIAGFPEREY ELRQTGKPLE 2050 2060 2070 2080 2090 2100 VKKSEVPPVS KDVVATEGKS MCRGLRNYNP IATSICKLVN ESDGHSETIH GIGFGPVIIT 2110 2120 2130 2140 2150 2160 NSHLFRRNNG TLQIQTHHGV FRVKNSTQLQ VSHMAKKDMI IIKMPCDVPP FPSKLRFRQP 2170 2180 2190 2200 2210 2220 EQGEKAVLVG SLFQQKSITS SVSESTMVMP VNDSGYWRHW VSTKDGDCGL PLVSTVDGAI 2230 2240 2250 2260 2270 2280 LGLHGLTSTK SDRNYFVPFD EQFERDILAN LEKLDWKRHW LHSSDLIAWG GMSLKENHPH 2290 2300 2310 2320 2330 2340 DCFRTSKLVT DLLGLTKDSV EYQSGQDKWV LAGLENNLKA VAQSESQLVT KHVVKGQCMY 2350 2360 2370 2380 2390 2400 FQEYLATHST AEKFFKPLMG AYQPSKLNKE AFTKDLYKYQ NEIIVGEVDK DAFDNAVEAV 2410 2420 2430 2440 2450 2460 IYLLDDLGFG ECAYVTDEEA ILDSLNMKAA VGALYKGKKK EYFESLSEPE KHHIVQASCE 2470 2480 2490 2500 2510 2520 RLFYGEMGVW NGSLKAELRP KEKVALNKTR TFTAAPIDTL LGGKCCVDDF NNRFYSLNIE 2530 2540 2550 2560 2570 2580 GPWTVGMTKF YGGWDKLMRK LPDGWRYCHA DGSQFDSSLT PFLLNAVLAV RLMFMEDWWV 2590 2600 2610 2620 2630 2640 GEQMLRNFYT EIIYTPILTP DGTIVKKFKG NNSGQPSTVV DNTLMVMIAM FYGMKKLNWT 2650 2660 2670 2680 2690 2700 DEQIKERIVF FAXGDDLIIA VQPEHEGILD TLQRSLGELG LKYDFSERCD DRQELWFMSH 2710 2720 2730 2740 2750 2760 QGHLVDGMYI PKLEQERIVS ILEWDRSTVI EHRAEAICAA MIEAWGYPEL LKQIRLFYAW 2770 2780 2790 2800 2810 2820 ILDHDMFKSL VAEGKLPYIA ETALRKLYTD ADATDVELEE YILRFTEVDE DEDHNDEVRY 2830 2840 2850 2860 2870 2880 QSGENKSKVE VDAAAAKLKE KEKEKHKKTE EGTSEGTSQT KEPDVDTGSQ GIVYVPKLAK 2890 2900 2910 2920 2930 2940 ITKKMRMPMV GGQVILHIPH LLDYKPEQVD LSNTRSSQQQ FTAWYNGLKE AYEITDDTSM 2950 2960 2970 2980 2990 3000 SVLMNGLMVW CIENGTSPNI NGNWTMMDGH EQNEYPLKPV IENAKPTFRQ IMHHFSDAAE 3010 3020 3030 3040 3050 3060 AYIEMRNAEK PYMPRYGLQR NLRDFSYARI AFDFYEITSR TSAKAREIHM QMKAAALNNV 3070 3080 3090 AIKTFGLDGN VGTQDEDTER HTANDVNRNM HSLLGMRQM

References

[1]	"The complete nucleotide sequence of peanut mottle virus (M strain) genomic RNA." Flasinski S., Gonzales R.A., Cassidy B.G. Submitted (SEP-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[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
EMBL GenBank DDBJ	AF023848 Genomic RNA. Translation: AAB94595.1.
3D structure databases
SMR	O56075. Positions 2066-2279.
ModBase	Search...
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-dir_pol_picornavirus. IPR007094. RNA-dir_pol_PSvirus. IPR009003. Ser/Cys_Pept_Trypsin-like. [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_PEMVM

Accession

Primary (citable) accession number: O56075

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1999
Last sequence update:	June 1, 1998
Last modified:	January 19, 2010
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)