Reviewed, UniProtKB/Swiss-Prot Q05057 (POLG_PYFV1)

Names and origin

Protein names	Recommended name:     Genome polyprotein Cleaved into the following 7 chains:     1- Recommended name:             Putative leader protein     2- Recommended name:             Capsid protein 1                 Short name=CP-1         Alternative name(s):             22.5 kDa protein             Coat protein 1     3- Recommended name:             Capsid protein 2                 Short name=CP-2         Alternative name(s):             26 kDa protein             Coat protein 2     4- Recommended name:             Capsid protein 3                 Short name=CP-3         Alternative name(s):             31 kDa protein             Coat protein 3     5- Recommended name:             Putative helicase               EC=3.6.1.-         Alternative name(s):             Putative NTP-binding protein     6- Recommended name:             Probable picornain 3C-like protease                 Short name=3C-like protease               EC=3.4.22.-     7- Recommended name:             Probable RNA-directed RNA polymerase               EC=2.7.7.48
Organism	Parsnip yellow fleck virus (isolate P-121) (PYFV) [Complete proteome]
Taxonomic identifier	33762 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Sequiviridae › Sequivirus
Virus host	Daucus carota (Carrot) [TaxID: 4039] Pastinaca sativa (Parsnip) [TaxID: 4041] Apium graveolens (Celery) [TaxID: 4045] Coriandrum sativum (Coriander) [TaxID: 4047] Anthriscus cerefolium (chervil) [TaxID: 40888] Heracleum sphondylium [TaxID: 40919] Anethum graveolens (dill) [TaxID: 40922] Aethusa cynapium (Fool's parsley) [TaxID: 40954] Anthriscus sylvestris [TaxID: 48027] Torilis japonica [TaxID: 49576] Chaerophyllum temulum [TaxID: 105274] Oenanthe aquatica [TaxID: 305795]

Protein attributes

Sequence length	3027 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Picornain 3C-like protease is a thiol protease that probably cleaves the polyprotein By similarity.
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subcellular location	Capsid protein 1: Virion Potential. Capsid protein 2: Virion Potential. Capsid protein 3: Virion Potential. Putative helicase: Host membrane; Multi-pass membrane protein Potential.
Post-translational modification	Specific enzymatic cleavages by picornain 3C-like protease in vivo yield mature proteins. Picornain 3C-like protease is autocatalytically processed By similarity.
Sequence similarities	Contains 1 peptidase C3 domain. Contains 1 RdRp catalytic domain. Contains 1 SF3 helicase domain.

Ontologies

Keywords
Biological process	RNA replication
Cellular component	Capsid protein Membrane Virion
Domain	Transmembrane
Ligand	ATP-binding Nucleotide-binding
Molecular function	Helicase Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	transcription, RNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW 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 – 394	394	Putative leader protein		PRO_0000041133
	Chain	395 – 588	194	Capsid protein 1		PRO_0000041134
	Chain	589 – 810	222	Capsid protein 2		PRO_0000041135
	Chain	811 – ?1069	259	Capsid protein 3 By similarity		PRO_0000041136
	Chain	?1070 – ?2006	937	Putative helicase Potential		PRO_0000041137
	Chain	?2007 – ?2214	208	Probable picornain 3C-like protease By similarity		PRO_0000041138
	Chain	?2215 – 3027	813	Probable RNA-directed RNA polymerase By similarity		PRO_0000041139
Regions
	Transmembrane	1183 – 1203	21	Potential
	Transmembrane	1210 – 1230	21	Potential
	Transmembrane	2907 – 2927	21	Potential
	Domain	1441 – 1607	167	SF3 helicase
	Domain	2516 – 2645	130	RdRp catalytic
	Nucleotide binding	1467 – 1474	8	ATP Potential
	Compositional bias	1088 – 1091	4	Poly-Glu
	Compositional bias	1829 – 1832	4	Poly-Thr
Sites
	Active site	2033	1	For picornain 3C-like protease activity Potential
	Active site	2068	1	For picornain 3C-like protease activity Potential
	Active site	2155	1	For picornain 3C-like protease activity Potential
	Site	394 – 395	2	Cleavage
	Site	588 – 589	2	Cleavage
	Site	810 – 811	2	Cleavage
Natural variations
	Natural variant	397	1	I → F
	Natural variant	962	1	T → I
	Natural variant	1373	1	L → F

Sequences

	Sequence		Length	Mass (Da)
	Q05057-1 [UniParc]. Last modified February 1, 1994. Version 1. Checksum: 0C41EB985F405BE2	FASTA	3,027	336,247
	10 20 30 40 50 60 MSSSNSQNSV NMVDGVDLND PTAVAIAAAS GTWGELDRAS TCMYNFFDVS DVERNPGESS 70 80 90 100 110 120 KQLVSRIKKR AGALLGVSRA FKDTEQVLSA ERCAFKSFSD DEEIMATTFE PLKDRAEITP 130 140 150 160 170 180 TAASKLDKTL EAHRAKFNYM AIDSIRVAVT SLMHQGDSRE CIMYLCDRRF KDPLLGAIAL 190 200 210 220 230 240 IGFTLPGMQT HVYKTGRMMA FSRKEAIAAD RLQLYLYVKG AKLERTQNTP ITVNVRTSLI 250 260 270 280 290 300 FGSNAENLLK CDSQIDTDMN IVSFMAQNQD LFGWLEAAQG GGYVPQSLRS ATTHTSNSVL 310 320 330 340 350 360 LHKWNNPVGS VSQRIASRMI FTKAIDAGTS YEDSDVVGSN AKCPNSIGKN LRIGVAQASI 370 380 390 400 410 420 QNTKDDSTPY SLADFVQDGP IAPVVASLES FMSSPSISQT LPLINDQFTR PIYSRTFEWK 430 440 450 460 470 480 ATDTVGASIF QLELPGDVVG PQASSLFSDT MQRAFCFSSD FELSILLTGN ESYMGALKIV 490 500 510 520 530 540 TDQLRRFHEA KQDDARVFHS MPGRTVFAKD SDGIKIPIEF MSIHKAVSAH DSNSHNALSR 550 560 570 580 590 600 VEARVVTPLS HISLSSPVLS ITIQVFAKNV KADYMMWRSL ETTFPTANAT LPSAVGDNFG 610 620 630 640 650 660 RLRTSQSEIL STSQILGLLT ERAFLGTAKV QQDTGARVII AEFALHPMSS RNVDGTLLLS 670 680 690 700 710 720 QLAALSAMYA FWRGSLVLTF EINCSASTRG KLIVSVTPKG GVALAGITAS HQGYGAEFDL 730 740 750 760 770 780 GTSSTRSFTM PFVSTDEWES IGDDGIMSAF EGVWDCPVAN LLVLHPITSI AESTPSVDIR 790 800 810 820 830 840 CYLHPGPDFQ LRGRRHIGLR AASRPLSIAQ ASPVLSQVDF SLMASISIDA TEESVVVAVP 850 860 870 880 890 900 CAPWYSKEEV DYTLLQNPLH WASRMFTLWR GDIEYRFVVK EEALGDGWQS PISVWHNPNT 910 920 930 940 950 960 QLSKCKITKI SNKKISKETY HGKKFCLMQL KSIDIVAVDD RRFSWRLCKI LDTTKDTAGD 970 980 990 1000 1010 1020 STSPSVTQIT YTGHPPMSSQ TGVVCIKFPK NSIKGKLKVY SKPGENFEFR HLGGVPSLQV 1030 1040 1050 1060 1070 1080 SQMVKYKKPF QNSVPDVFIT PSKESSKKEL GFKPKVVESA AVPKLAVGQA QGLVSKIKGF 1090 1100 1110 1120 1130 1140 GSLWKFDEEE ETLNSELQKM AVEVSGEIDP IQDEGWAKRK INEIVSSVST KLIEASTSIL 1150 1160 1170 1180 1190 1200 SNAATRAIST LFDVMIGKVR GVLSSLVDSI SGAFKMCLGD PKCLCLIGIS ISAVLGYCTL 1210 1220 1230 1240 1250 1260 KLVENSVPDA LGIFKALMMV AITSISALYW PKAAISIVTK YEEQFKDIEN YCSTIYKHIF 1270 1280 1290 1300 1310 1320 LGVSEDKMEG ATPAKACATN FEDLAHGKAQ AGGKSFLELA GLIAYIRLCV VLCKAMNTSF 1330 1340 1350 1360 1370 1380 LEPFTPSNME KQCRTVGGIS IGVKTLCEFK DYIYRMIVGG ITPTSSYVKV SGLTGFDIRE 1390 1400 1410 1420 1430 1440 WFEEVESVTL QETRYTQMGS DEKIKQIRAL YDKGVNVMGK LTMIDSPHLS RVCERSFRLC 1450 1460 1470 1480 1490 1500 KELLDETHRC KGASSTRVDP FHVSLYGSPG VGKSFVMGKL LDDVLDFMSE PQADRCYSKT 1510 1520 1530 1540 1550 1560 PNEEYWSGYI GQTAVKCDDL GQDLSKGFSP TYNQIIQMKT NNCFIVPMAD LANKGRTFTS 1570 1580 1590 1600 1610 1620 KYIFSTTNVP GCGTKHGLAD PGAFMRRRNI FVEVETEGDM IPGSTNHMRF TLLNPLNPDE 1630 1640 1650 1660 1670 1680 RIMKYPARMK YVDFLCVCVA EARVYFETQN LVMETLNGTT KNQEEPSKDV IAILEELGDG 1690 1700 1710 1720 1730 1740 VVEGILEKRK ELLSQFGVMD PPPFDAIELE PGKAQASVCF STDAFGNPLK NPFVELFGKL 1750 1760 1770 1780 1790 1800 RDEFERATKQ EMPDDILTKF GASLTLGEPT VFGYENQCGM HSAKDSNLMS SFFTFIFGKN 1810 1820 1830 1840 1850 1860 LIYKQEQEFL RHIDTLSSMG VLRLVDAVTT TTKGDKKILS FANIYDNQAF EQLGVLERLI 1870 1880 1890 1900 1910 1920 FHLVLATRAA KKGRINGIRE RLANWFTSAR ILSNNILEEL PSPIKMLLVL ATSVGSLYLA 1930 1940 1950 1960 1970 1980 FKGLSGIGSM ILGFTGNFTA KEEDFEMISL NALMGQAKSK GRNFITSGDE LTTRLSRMMS 1990 2000 2010 2020 2030 2040 RASLATGRAQ GGRSHMDTCE ALLARQGQIT NMATGLHLVA TDLGGGFLLA PLHTFAGAEK 2050 2060 2070 2080 2090 2100 DDIFRFQNGA DYYFAFEPKD VSQLSEYDAC IIRTDAIPMK SSIVSIFAKE SQIELLVDMS 2110 2120 2130 2140 2150 2160 AHFVCGPWKV PFGGEFISEQ TVAKRIASFK YFMDEKLYMA INGWSSPFKT EDGQCGSCLV 2170 2180 2190 2200 2210 2220 STSDKLDGKV FCSLVAGTYD RVTGKYVSTY VPITCDMIKK SISLLTGAEF SESQSSICDS 2230 2240 2250 2260 2270 2280 PISDTVAETI KVDQLFSSKP GASGKFGVFG VNDTIGIIDV VGRTFPETTP KSITKSTIVP 2290 2300 2310 2320 2330 2340 SLIQPYMPRK PLTEPAILDP RDVRLGENRY DPMIDGIKKY EEQARPIKIS WRNQIIESMA 2350 2360 2370 2380 2390 2400 AQMQDWETFM VREGYMTMDL PMSVVINGID GVEYYEPLNM STSEGYPLIL NRPKDAHGKE 2410 2420 2430 2440 2450 2460 YLFETMESGE RRIKSAKLEA HYESYGHALQ STEPFPLICI ECPKDERRAL DKIYEKPKTR 2470 2480 2490 2500 2510 2520 LFSILPVEFN MHARRLFLDF NVFVMANRHK HGIMVGINPH SREWSDLAIS LASFSPYGFN 2530 2540 2550 2560 2570 2580 GDFANFDGMF HPSSFSMVSE LANIFYGNFL STERDNLTRM LTNRFSLMKG AILRVPGGGP 2590 2600 2610 2620 2630 2640 SGFPMTVIFN SFINLFYLQS AWIMLARFNG RQDISHPCNF PKYVRACVYG DDNIVAIKME 2650 2660 2670 2680 2690 2700 VLPWYNLQTV SEALFDYFGV TMTDGAKNKA SEAKPYGKIL EFDFLKRHFK ADELIPSLFH 2710 2720 2730 2740 2750 2760 APLHKRSIEE QVYWIREGGN SLELLEANIE NALYEAHHHG REYYEELKDQ IKKAMNRAGY 2770 2780 2790 2800 2810 2820 MSFVAPSYLM CRQRWLQQDL GEVATSSLPS HVGLLKEATK NHFSALTGQE EIKAIFEEID 2830 2840 2850 2860 2870 2880 NGNGGTTKHG NMQQILPNIF IGPTRIFETK YGNSLFNLVC DNSLSKGQTR YGVKHGIQSL 2890 2900 2910 2920 2930 2940 SKPDFTYISE SLPCLTTPNF RMVCLDPIGG ELALATALCL LHAAGIINTK TFTMFMRIHI 2950 2960 2970 2980 2990 3000 KQWKHVLQAY FRVCETFVSK EWQNFKRDIK RLSQDDVGCS RTTPVCGRFL TLDGQLPQHI 3010 3020 KSLDKIDFKK TRRIKIAQDE DFIIQID

References

[1]	"The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus." Turnbull-Ross A.D., Reavy B., Mayo M.A., Murant A.F. J. Gen. Virol. 73:3203-3211(1992) [PubMed: 1469358] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Sequence analysis of the parsnip yellow fleck virus polyprotein: evidence of affinities with picornaviruses." Turnbull-Ross A.D., Mayo M.A., Reavy B., Murant A.F. J. Gen. Virol. 74:555-561(1993) [PubMed: 8468549] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN, PROTEIN SEQUENCE OF 395-404; 589-598 AND 811-820.

Cross-references

Sequence databases
EMBLGenBankDDBJ	D14066 Genomic RNA. Translation: BAA03151.1.
PIR	JQ1917.
RefSeq	NP_619734.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	940238.
Family and domain databases
InterPro	IPR000605. Helicase_SF3_ssDNA/RNA_vir. IPR014759. Helicase_SF3_ssRNA_vir. IPR001676. Picornavirus_capsid. IPR001205. RNA_pol_P3D. IPR007094. RNA_pol_PSvir. [Graphical view]
Pfam	PF00680. RdRP_1. 1 hit. PF00073. Rhv. 1 hit. PF00910. RNA_helicase. 1 hit. [Graphical view]
PROSITE	PS50507. RDRP_SSRNA_POS. 1 hit. PS51218. SF3_HELICASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_PYFV1

Accession

Primary (citable) accession number: Q05057

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1994
Last modified:	June 16, 2009
This is version 60 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)