Reviewed, UniProtKB/Swiss-Prot P17767 (POLG_PPVRA)

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	Plum pox potyvirus (strain Rankovic) (PPV) [Complete proteome]
Taxonomic identifier	12214 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Prunus domestica (Garden plum) [TaxID: 3758] Prunus persica (Peach) [TaxID: 3760] Prunus cerasifera (cherry plum) [TaxID: 36595] Prunus armeniaca (Apricot) [TaxID: 36596] Prunus salicina [TaxID: 88123] Prunus glandulosa [TaxID: 105665] Prunus spinosa (Blackthorn) [TaxID: 114937]

Protein attributes

Sequence length	3140 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 By similarity. 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 – 308	308	P1 proteinase Potential		PRO_0000040341
	Chain	309 – 766	458	Helper component proteinase Potential		PRO_0000040342
	Chain	767 – 1116	350	Protein P3 By similarity		PRO_0000040343
	Chain	1117 – 1168	52	6 kDa protein 1 By similarity		PRO_0000040344
	Chain	1169 – 1803	635	Cytoplasmic inclusion protein By similarity		PRO_0000040345
	Chain	1804 – 1856	53	6 kDa protein 2 By similarity		PRO_0000040346
	Chain	1857 – 2049	193	Viral genome-linked protein By similarity		PRO_0000040347
	Chain	2050 – 2292	243	Nuclear inclusion protein A By similarity		PRO_0000040348
	Chain	2293 – 2810	518	Nuclear inclusion protein B By similarity		PRO_0000040349
	Chain	2811 – 3140	330	Coat protein By similarity		PRO_0000040350
Regions
	Domain	1240 – 1392	153	Helicase ATP-binding
	Domain	1411 – 1570	160	Helicase C-terminal
	Domain	2534 – 2658	125	RdRp catalytic
	Nucleotide binding	1253 – 1260	8	ATP Potential
	Motif	360 – 363	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	618 – 620	3	Involved in virions binding and aphid transmission By similarity
	Motif	1342 – 1345	4	DECH box
	Motif	1897 – 1904	8	Nuclear localization signal Potential
Sites
	Active site	216	1	For P1 proteinase activity By similarity
	Active site	225	1	For P1 proteinase activity Potential
	Active site	259	1	For P1 proteinase activity By similarity
	Active site	652	1	For helper component proteinase activity By similarity
	Active site	725	1	For helper component proteinase activity By similarity
	Active site	2095	1	For nuclear inclusion protein A activity By similarity
	Active site	2130	1	For nuclear inclusion protein A activity By similarity
	Active site	2200	1	For nuclear inclusion protein A activity By similarity
	Site	308 – 309	2	Cleavage; by P1 proteinase Potential
	Site	766 – 767	2	Cleavage; by HC-pro Potential
	Site	1116 – 1117	2	Cleavage; by NIa-pro By similarity
	Site	1168 – 1169	2	Cleavage; by NIa-pro By similarity
	Site	1803 – 1804	2	Cleavage; by NIa-pro By similarity
	Site	1856 – 1857	2	Cleavage; by NIa-pro By similarity
	Site	2049 – 2050	2	Cleavage; by NIa-pro By similarity
	Site	2292 – 2293	2	Cleavage; by NIa-pro By similarity
	Site	2810 – 2811	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1919	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	P17767-1 [UniParc]. Last modified February 1, 1994. Version 2. Checksum: 5F3DBB07982CF3F5	FASTA	3,140	355,581
	10 20 30 40 50 60 MSTIVFGSFT CHLDAAIHQD NADRLAKAWT RPENRQVSNV HLLCRRAAKS LINTYESATA 70 80 90 100 110 120 SAWKGLEEKL QPMFAKREFS KTVTKRKGLR CFKESSEKFI EKKLRKQYQE ERERFQFLNG 130 140 150 160 170 180 PDAIVNQISV DKCEASVRVP FPHIIEKPSF ATPSMKKKVV FTKVRMSEAS LQLFMRRVAA 190 200 210 220 230 240 NAKANGQKVE IIGRKRVVGN YTTKSRLTYF RTHVRHLDGS KPRYDLVLDE ATKKILQLFA 250 260 270 280 290 300 NTSGFHHVHK KGEVTPGMSG FVVNPMNLSD PMQVYDTDLF IVRGKHNSIL VDSRCKVSKE 310 320 330 340 350 360 QSNEIIHYSD PGKQFWDGFT NSFMQCKLRE TDHQCTSDLD VKECGYVAAL VCQAIIPCGK 370 380 390 400 410 420 ITCLQCAQKY SYMSQQEIRD RFSTVIEQHE KTVMDNYPQF SHVLAFLKRY RELMRVENQN 430 440 450 460 470 480 YEAFKDITHM IGERKEAPFS HLNKINELII KGGMMSAQDY IEASDHLREL ARYQKNRTEN 490 500 510 520 530 540 IRSGSIKAFR NKISSKAHVN MQLMCDNQLD TNGNFVWGQR EYHAKRFFRN YFDVIDVSEG 550 560 570 580 590 600 YRRHIVRENP RGIRKLAIGN LVMSTNLAAL RKQLLGEECI HFEVSKECTS KRGENFVYQC 610 620 630 640 650 660 CCVTHEDGTP LESEIISPTK NHLVVGNSGD SKYVDLPTAK GGAMFIAKAG YCYINIFLAM 670 680 690 700 710 720 LININEDEAK SFTKTVRDTL VPKLGTWPSM MDLATACHFL AILYPETRNA ELPRILVDHE 730 740 750 760 770 780 AKIFHVVDSF GSLSTGMHVL KANTINQLIS FASDTLDSNM KTYLVGGLEV DKCDEFKNVK 790 800 810 820 830 840 LLIRSIYKPQ IMEQVLKEEP YLLLMSVLSP GVLMALFNSG SLEKATQYWI TRSHSLAAIT 850 860 870 880 890 900 SMLSSLAAKV SLASTLNAQM SVIDEHAAVL CDSVFVGTKP YASYMMAVKT LERMKARTES 910 920 930 940 950 960 DHTLNDLGFS VIRQATPHLV EKSYLQELEQ AWKELSWSEK FSAILESQRW RKHIPKPFIP 970 980 990 1000 1010 1020 KDGADLGGRY DISVRSLLGN QYKRLRDVVR RKRDDVVCYT HQSMGKLFCK AIGISTSFLP 1030 1040 1050 1060 1070 1080 STLKMFDMLI VFSLLLSIGA TCNSMINEHK HLKQLAADRE DKKRFKRLQV LHTRLSEKVG 1090 1100 1110 1120 1130 1140 CTPTADEFLE YVGGENPDLL KHAEDLIGDG QVVVHQSKRD SQANLERVVA FVALVMMLFD 1150 1160 1170 1180 1190 1200 SERSDGVYKI LNKLKGIMGS VDQAVQHQSL DDIEDILDEK KLTVDFVLQS NEVAPTVPFD 1210 1220 1230 1240 1250 1260 STFEKWWTNQ LETGNVIPHY RTEGHFLEFT RENAAHIANE VMHGSHQDIL IRGAVGSGKS 1270 1280 1290 1300 1310 1320 TGLPFHLSKK GHVLLIEPTR PLAENVCKQL RGQPFNVNPT LRMRGMSTFG STPITVMTSG 1330 1340 1350 1360 1370 1380 YALHFLANNP TYLDNYKCII FDECHVHDAS AMAFRCLLSE YSYPGKILKV SATPPGHEVD 1390 1400 1410 1420 1430 1440 FKTQKEVKVI VEESLSFQQF VSNLGTGCNS DILKHGVNVL VYVASYNEVD TLSKLLTDRS 1450 1460 1470 1480 1490 1500 FKVSKVDGRT MKIGNVEIPT SGTQAKPHFV VATNIIENGV TLDIDVVVDF GLKVVPVLDI 1510 1520 1530 1540 1550 1560 DNRLVRYTKK SISYGERIQR LGRVGRNKPG AALRIGFTEK GLTQIPPIIA TEAAFLCFTY 1570 1580 1590 1600 1610 1620 GLPVMTNGVS TSLLAMCTVK QARTMQQFEL SPFYTVALVR FDGTMHQEIF RLLKSYRLRD 1630 1640 1650 1660 1670 1680 SEVILNKLAI PNSNVCGWMS VRDYKRQGCN LDLDENIRVP FYVKDIPETL HERIWQVVET 1690 1700 1710 1720 1730 1740 HKSDAGFGRI CSSSACKIAY TLQTDIHSIP RTIKIIDALL EQERTKQAHF RAMTSQSCSS 1750 1760 1770 1780 1790 1800 SNFSLSSITS AIRSKYAKDH TEENIGVLQT AKSQLLEFKN LNIDPSYPEL VRNFGALECV 1810 1820 1830 1840 1850 1860 HHQTKEGVSK ALQLKGHWNK RLITRDATLM LGVLGGGAWM IFSYLRDSFK EEVVHQGFNR 1870 1880 1890 1900 1910 1920 RQRQKLKFRQ ARDNRMAREV YGDDSTMADY FGSAYSKKGK SKGKTRGMGT KTRKFVNMYG 1930 1940 1950 1960 1970 1980 YDPTDYNFVR FVDPLTGHTL DENPLMDINL VQEHFSQIRN DYIGDDKITM QHIMSNPGIV 1990 2000 2010 2020 2030 2040 AYYIKDATQK ALKVDLTPHN PLRVCDKTAT IAGFPEREFE LRQTGHPVFV EPNAIPKINE 2050 2060 2070 2080 2090 2100 EGDEEVDHES KSLFRGLRDY NPIASSICQL NNSSGARQSV MFGLGFGGLI VTNQHLFKRN 2110 2120 2130 2140 2150 2160 DGELTIRSHH GEFVVKDTKT LKLLPCKGRD IVIIRLPKDF PPFPKRLQFR TPTTEDRVCL 2170 2180 2190 2200 2210 2220 IGSNFQTKSI SSTMSETSAT YPVDNSHFWK HWISTKDGHC GLPIVSTRDG SILGLHSLAN 2230 2240 2250 2260 2270 2280 STNTQNFYAA FPDNFETTYL SNQDNDNWIK QWRYNPDEVC WGSLQLKRDI PQSPFTICKL 2290 2300 2310 2320 2330 2340 LTDLDGEFVY TQSKTTHWLR DRLEGNLKAV GACPGQLVTK HVVKGKCTLF ETYLLTHPEE 2350 2360 2370 2380 2390 2400 HEFFRPLMGA YQKSALNKDA YVKDLMKYSK PIVVGAVDCD QFERAVDVVI SMLISKGFEE 2410 2420 2430 2440 2450 2460 CNYVTDPDDI FSALNMKAAV GALYSGKKRD YFKNVSDQDK ESFVRASCKR LFMGKKGVWN 2470 2480 2490 2500 2510 2520 GSLKAELRPK EKVEANKTRS FTAAPIDTLL GGKVCVDDFN NQFYSLNLHC PWSVGMTKFR 2530 2540 2550 2560 2570 2580 GGWDKLLRAL PEGWIYCDAD GSQFDSSLSP YLINAVLNIR LAFMEEWDIG EQMLSNLYTE 2590 2600 2610 2620 2630 2640 IVYTPIATPD GTIVKKFKGN NSGQPSTVVD NTLMVILAMT YSLLKLGYHP DTHDCICRYF 2650 2660 2670 2680 2690 2700 VNGDDLVLAV HPAYESIYDE LQEHFSQLGL NYTFATKTEN KEELWFMSHK GVLYDDMYIP 2710 2720 2730 2740 2750 2760 KLEPERIVSI LEWDRSNEPI HRLEAICASM VEAWGYKELL REIRKFYSWV LEQAPYNALS 2770 2780 2790 2800 2810 2820 KDGKAPYIAE TALKKLYTDT EASETEIERY LEAFYDDFND DGESNVVVHQ ADEREDEEEV 2830 2840 2850 2860 2870 2880 DAGKPSVVTA PAATSPILQP PPVIQPAPRT TASMLNPIFT PATTQPATKP VSQVSQPQLQ 2890 2900 2910 2920 2930 2940 TFGTYGNEDA SPSNSNALVN TNRDRDVDAG SVGTFTVPRL KAMTSKLSLP KVKGKAIMNL 2950 2960 2970 2980 2990 3000 NHLAHYSPAQ VDLSNTRAPQ SCFQTWYEGV KRDYDVTDDE MSIILNGLMV WCIENGTSPN 3010 3020 3030 3040 3050 3060 INGMWVMMDG ETQVEYPIKP LLDHAKPTFR QIMAHFSNVA EAYIEKRNYE KAYMPRYGIQ 3070 3080 3090 3100 3110 3120 RNLTDYSLAR YAFDFYEMTS TTPVRAREAH IQMKAAALRN VQNRLFGLDG NVGTQEEDTE 3130 3140 RHTAGDVNRN MHNLLGVRGV

References

[1]	"The complete nucleotide sequence of plum pox potyvirus RNA." Lain S., Riechmann J.L., Garcia J.A. Virus Res. 13:157-172(1989) [PubMed: 2773595] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[2]	"Proteolytic activity of the plum pox potyvirus NIa-like protein in Escherichia coli." Garcia J.A., Riechmann J.L., Lain S. Virology 170:362-369(1989) [PubMed: 2658302] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1778-2342.
[3]	"Nucleotide sequence of the 3' terminal region of plum pox potyvirus RNA." Lain S., Riechmann J.L., Mendez E., Garcia J.A. Virus Res. 10:325-342(1988) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2263-3140.
[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	M21847 Genomic RNA. Translation: AAA85458.1. M26965 mRNA. Translation: AAA47085.1.
PIR	GNVSRA. A60009.
3D structure databases
SMR	P17767. Positions 1244-1563, 2058-2271.
ModBase	Search...
Family and domain databases
InterPro	IPR014001. DEAD-like_N. IPR001650. DNA/RNA_helicase_C. 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	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_PPVRA

Accession

Primary (citable) accession number: P17767

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	February 1, 1994
Last modified:	February 9, 2010
This is version 98 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)