Reviewed, UniProtKB/Swiss-Prot Q01901 (POLG_PRSVH)

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	Papaya ringspot virus (strain P / mutant HA) [Complete proteome]
Taxonomic identifier	31731 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Carica papaya (Papaya) [TaxID: 3649]

Protein attributes

Sequence length	3344 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 – 547	547	P1 proteinase By similarity		PRO_0000040361
	Chain	548 – 1004	457	Helper component proteinase By similarity		PRO_0000040362
	Chain	1005 – 1349	345	Protein P3 By similarity		PRO_0000040363
	Chain	1350 – 1401	52	6 kDa protein 1 By similarity		PRO_0000040364
	Chain	1402 – 2036	635	Cytoplasmic inclusion protein By similarity		PRO_0000040365
	Chain	2037 – 2093	57	6 kDa protein 2 By similarity		PRO_0000040366
	Chain	2094 – 2282	189	Viral genome-linked protein By similarity		PRO_0000040367
	Chain	2283 – 2520	238	Nuclear inclusion protein A By similarity		PRO_0000040368
	Chain	2521 – 3057	537	Nuclear inclusion protein B By similarity		PRO_0000040369
	Chain	3058 – 3344	287	Coat protein By similarity		PRO_0000040370
Regions
	Domain	1473 – 1625	153	Helicase ATP-binding
	Domain	1644 – 1803	160	Helicase C-terminal
	Domain	2761 – 2885	125	RdRp catalytic
	Nucleotide binding	1486 – 1493	8	ATP Potential
	Motif	598 – 601	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	856 – 858	3	Involved in virions binding and aphid transmission By similarity
	Motif	1575 – 1578	4	DECH box
	Motif	2134 – 2141	8	Nuclear localization signal Potential
Sites
	Active site	456	1	For P1 proteinase activity By similarity
	Active site	465	1	For P1 proteinase activity Potential
	Active site	499	1	For P1 proteinase activity By similarity
	Active site	890	1	For helper component proteinase activity By similarity
	Active site	963	1	For helper component proteinase activity By similarity
	Active site	2327	1	For nuclear inclusion protein A activity By similarity
	Active site	2362	1	For nuclear inclusion protein A activity By similarity
	Active site	2431	1	For nuclear inclusion protein A activity By similarity
	Site	547 – 548	2	Cleavage; by P1 proteinase Potential
	Site	1004 – 1005	2	Cleavage; by HC-pro Potential
	Site	1349 – 1350	2	Cleavage; by NIa-pro By similarity
	Site	1401 – 1402	2	Cleavage; by NIa-pro By similarity
	Site	2036 – 2037	2	Cleavage; by NIa-pro By similarity
	Site	2093 – 2094	2	Cleavage; by NIa-pro By similarity
	Site	2282 – 2283	2	Cleavage; by NIa-pro By similarity
	Site	2520 – 2521	2	Cleavage; by NIa-pro By similarity
	Site	3057 – 3058	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	2156	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q01901-1 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: E90CD7523AC5243D	FASTA	3,344	381,046
	10 20 30 40 50 60 MSSLYTLRAA AQYDRRLESK KGSGWVEHKL ERKGERGNTH YCSEFDISKG AKILQLVQIG 70 80 90 100 110 120 NTEVGRTFLE GNRFVRANIF EIIRKTMVGR LGYDFESELW VCRNCDKTSE KYFKKCDCGE 130 140 150 160 170 180 TYYYSERNLM RTMNDLMYQF DMTPSEINSV DLEYLANAVD YAEQLVKRSQ VPEPVELAMM 190 200 210 220 230 240 EPIVASGEGI LMVSEPEVMP VTTKVEEAWT IQIGEIPVPL VVIKETPVIS GVEGTLNSTG 250 260 270 280 290 300 FSLEADITKL VEKEILQEEV KEAVHLALEV GNEIAEKKPE LKLIPYWSAS LELHKRIRKH 310 320 330 340 350 360 KEHAKIAAIQ VQKEREKDQK VFSALELRLN LKSRRRNQAV VCDKRGTLKW ETQRGHKKSK 370 380 390 400 410 420 LMQQASDFVV TQIHCDFGCK TQYSEPHIPG IKQSTSKKIC KPRKHSRIVG NSKINYIMKN 430 440 450 460 470 480 LCDTIIERGI PVELVTKRCK RRILQKEGRS YVQLRHMNGI RARQDVSSSP DMELLFTQFC 490 500 510 520 530 540 KFLVGHKPLK SKNLTFGSSG LIFKPKFADN VGRYFGDYFV VRGRLGGKLF DGRSKLARSV 550 560 570 580 590 600 YAKMDQYNDV AEKFWLGFNR AFLRHRKPTD HTCTSDMDVT MCGEVAALAT IILFPCHKIT 610 620 630 640 650 660 CNTCMSKVKG RVIDEVGEDL NCELERLRET LSAYGGSFGH VSTLLDQLNR VLNARNMNDG 670 680 690 700 710 720 AFKEIAKKID EKKESPWTHM TTINNTLYKG SLATGYEFER ASNSLREIVR WHLKRTESIK 730 740 750 760 770 780 AGSVESFRNK RSGKAHFNPA LTCDNQLDKN GNFLWGERQY HAKRFFANYF EKIDHSKGYE 790 800 810 820 830 840 YYSQRQNPNG IRKIAIGNLV FSTNLERFRQ QMVEHHIDQG PITRECIALR NNNYVHVCSC 850 860 870 880 890 900 VTLDDGTPAT SELKTPTKNH IVLGNSGDPK YVDLPTLESD SMYIAKKGYC YMNIFLAMLI 910 920 930 940 950 960 NIPENEAKDF TKRVRDLVGS KLGEWPTMLD VATCANQLVV FHPDAANAEL PQILVDHRQK 970 980 990 1000 1010 1020 TMHVIDSFGS VDSGYHILKA NTVNQLIQFA RDPLDSEMKH YIVGGEFDPT TNCLHQLIRV 1030 1040 1050 1060 1070 1080 IYKPHELRSL LRNEPYLIVI ALMSPSVLLT LFNSGAVEHA LNYWIKRDQD VVEVIVLVEQ 1090 1100 1110 1120 1130 1140 LCRKVTLART ILEQFNEIRQ NARDLHELMD RNNKPWISYD RSLELLSVYA NSQLTDEGLL 1150 1160 1170 1180 1190 1200 KQGFSTLDPR LREAVEKTYA TLLQEEWRAL SLFQKLHLRY FAFKSQPSFS EYLKPKGRAD 1210 1220 1230 1240 1250 1260 LKIVYDFSPK YCVHEVGKAF LLPVKAGAKI ASRIINGCGA FIRKSAAKGC AYIFKDLFQF 1270 1280 1290 1300 1310 1320 VHVVLVLSIL LQIFRSAQGI ATEHLQLKQA KAEVERQKDF DRLEALYAEL CVKSGEQPTT 1330 1340 1350 1360 1370 1380 EEFLDFVMER EPRLKDQAYN LIYIPVIHQA KSDNEKKLEQ VIAFITLILM MIDVDKSDCV 1390 1400 1410 1420 1430 1440 YRILNKFKGV INSSNTNVYH QSLDDIRDFY EDKQLTIDFD ITGENQINRG PIDVTFEKWW 1450 1460 1470 1480 1490 1500 DNQLSNNNTI GHYRIGGTFV EFSRVNAATV ASEIAHSPER EFLVRGAVGS GKSTNLPFLL 1510 1520 1530 1540 1550 1560 SKHGSVLLIE PTRPLCENVC KQLRGEPFHC NPTIRMRGLT AFGSTNITIM TSGFALHYYA 1570 1580 1590 1600 1610 1620 HNIQQLRLFD FIIFDECHVI DSQAMAFYCL MEGNAIEKKI LKVSATPPGR EVEFSTQFPT 1630 1640 1650 1660 1670 1680 KIVTEQSISF KQLVDNFGTG ANSDVTAFAD NILVYVASYN EVDQLSKLLS DKGYLVTKID 1690 1700 1710 1720 1730 1740 GRTMKVGKTE ISTSGTKFKK HFIVATNIIE NGVTLDIEAV IDFGMKVVPE MDSDNRMIRY 1750 1760 1770 1780 1790 1800 SKQAISFGER IQRLGRVGRH KEGIALRIGH TEKGIQEIPE MAATEAAFLS FTYGLPVMTH 1810 1820 1830 1840 1850 1860 NVGLSLLKNC TVRQARTMQQ YELSPFFTQN LVNFDGTVHP KIDVLLRPYK LRDCEVRLSE 1870 1880 1890 1900 1910 1920 AAIPHGVQSI WLSARDYEAV GGRLCLEGDV RIPFLIKDVP ERLYKELWDI VQTYKRDFTF 1930 1940 1950 1960 1970 1980 GRINSVSAGK IAYTLRTDVY SIPRTLITID KLIESENMKH AHFKAMTSCT GLNSSFSLLG 1990 2000 2010 2020 2030 2040 VINTIQSRYL VDHSVENIRK LQLAKAQIQQ LEAHMQENNV ENLIQSLGAV RAVYHQSVDG 2050 2060 2070 2080 2090 2100 FKHIKRELGL KGVWDGSLMI KDAIVCGFTM AGGAMLLYQH FRDKFTNVHV FHQGFSARQR 2110 2120 2130 2140 2150 2160 QKLRFKSAAN AKLGREVYGD DGTIEHYFGE AYTKKGNKKG KMHGMGVKTR KFVATYGFKP 2170 2180 2190 2200 2210 2220 EDYSYVRYLD PLTGETLDES PQTDISMVQD HFSDIRRKYM DSDSFDRQAL IANNTIKAYY 2230 2240 2250 2260 2270 2280 VRNSAKAALE VDLTPHNPLK VCDNKLTIAG FPDREAELRQ TGPPRTIQVD QVPPPSKSVH 2290 2300 2310 2320 2330 2340 HEGKSLCQGM RNYNGIASVV CHLKNTSGKG KSLFGIGYNS FIITNRHLFK ENNGELIVKS 2350 2360 2370 2380 2390 2400 QHGKFIVKNT TTLQIAPVGK TDLLIIRMPK DFPPFHSRAR FRAMKAGDKV CMIGVDYQEN 2410 2420 2430 2440 2450 2460 HIASKVSETS IISEGTGDFG CHWISTNDGD CGNPLVSVSD GFIVGLHSLS TSTGDQNFFA 2470 2480 2490 2500 2510 2520 KIPAQFEEKV LRKIDDLTWS KHWSYNINEL SWGALKVWES RPEAIFNAQK EVNQLNVFEQ 2530 2540 2550 2560 2570 2580 SGGRWLFDKL HGNLKGVSSA PSNLVTKHVV KGICPLFRNY LECDEEAKAF FSPLMGHYMK 2590 2600 2610 2620 2630 2640 SVLSKEAYIK DLLKYSSDIV VGEVNHDVFE DSVAQVIELL NDHECPELEY ITDSEVIIQA 2650 2660 2670 2680 2690 2700 LNMDAAVGAL YTGKKRKYFE GSTVEHRQAL VRKSCERLYE GRMGVWNGSL KAELRPAEKV 2710 2720 2730 2740 2750 2760 LAKKTRSFTA APLDTLLGAK VCVDDFNNWF YSKNMECPWT VGMTKFYKGW DEFLKKFPDG 2770 2780 2790 2800 2810 2820 WVYCDADGSQ FDSSLTPYLL NAVLSIRLWA MEDWDIGEQM LKNLYGEITY TPILTPDGTI 2830 2840 2850 2860 2870 2880 VKKFKGNNSG QPSTVVDNTL MVLITMYYAL RKAGYDTKTQ EDMCVFYING DDLCIAIHPD 2890 2900 2910 2920 2930 2940 HEHVLDSFSS SFAELGLKYD FAQRHRNKQN LWFMSHRGIL IDDIYIPKLE PERIVAILEW 2950 2960 2970 2980 2990 3000 DKSKLPEHRL EAITAAMIES WGYGDLTHQI RRFYQWVLEQ APFNELAKQG RAPYVSEVGL 3010 3020 3030 3040 3050 3060 RRLYTSERGS MDELEAYIDK YFERERGDSP ELLVYHESRG TDDYQLVCSN NTHVFHQSKN 3070 3080 3090 3100 3110 3120 EAVDAGLNEK LKEKEKQKEK EKEKQKEKEK DGASDGNDVS TSTKTGERDR DVNVGTSGTF 3130 3140 3150 3160 3170 3180 TVPRIKSFTD KMVLPRIKGK TVLNLNHLLQ YNPQQIDISN TRATHSQFEK WYEGVRNDYG 3190 3200 3210 3220 3230 3240 LNDNEMQVML NGLMVWCIEN GTSPDISGVW VMMDGETQVD YPIKPLIEHA TPSFRQIMAH 3250 3260 3270 3280 3290 3300 FSNAAEAYIA KRNATERYMP RYGIKRNLTD ISLARYAFDF YEVNSKTPDR AREAHMQMKA 3310 3320 3330 3340 AALRNTSRRM FGMDGSVSNK EENTERHTVE DVNRDMHSLL GMRN

References

[1]	"Comparison of the nuclear inclusion b protein and coat protein genes of five papaya ringspot virus strains distinct in geographic origin and pathogenicity." Wang C.H., Bau H.J., Yeh S.D. Phytopathology 84:1205-1210(1994) [Agricola: IND20450567] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Complete nucleotide sequence and genetic organization of papaya ringspot virus RNA." Yeh S.D., Jan F.J., Chiang C.H., Doong T.J., Chen M.C., Chung P.H., Bau H.J. J. Gen. Virol. 73:2531-2541(1992) [PubMed: 1402799] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	"Nucleotide sequence comparison of the 3'-terminal regions of severe, mild, and non-papaya infecting strains of papaya ringspot virus." Wang C.H., Yeh S.D. Arch. Virol. 127:345-354(1992) [PubMed: 1456896] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2561-3344.
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X67673 Genomic RNA. Translation: CAA47905.1. S46722 Genomic RNA. Translation: AAB23789.1. X67672 Genomic RNA. Translation: CAA47904.1.
PIR	JQ1899.
RefSeq	NP_056758.1.
3D structure databases
SMR	Q01901. Positions 1481-1787, 2291-2502.
ModBase	Search...
Protein family/group databases
MEROPS	C04.009.
Genome annotation databases
GeneID	1494043.
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_PRSVH

Accession

Primary (citable) accession number: Q01901

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1996
Last modified:	January 19, 2010
This is version 90 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)