Reviewed, UniProtKB/Swiss-Prot Q83034 (POLG_RTSVA)

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	Rice tungro spherical virus (strain A) (RTSV) (Rice tungro spherical waikavirus) [Complete proteome]
Taxonomic identifier	337081 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Sequiviridae › Waikavirus
Virus host	Oryza sativa (Rice) [TaxID: 4530]

Protein attributes

Sequence length	3473 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	Coiled coil 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 – 644	644	Putative leader protein Potential		PRO_0000041140
	Chain	645 – 852	208	Capsid protein 1		PRO_0000041141
	Chain	853 – 1055	203	Capsid protein 2		PRO_0000041142
	Chain	1056 – ?1366	311	Capsid protein 3		PRO_0000041143
	Chain	?1367 – 2526	1160	Putative helicase Potential		PRO_0000041144
	Chain	2527 – 2852	326	Probable picornain 3C-like protease Probable		PRO_0000041145
	Chain	2853 – 3473	621	Probable RNA-directed RNA polymerase By similarity		PRO_0000041146
Regions
	Transmembrane	1496 – 1516	21	Potential
	Transmembrane	1595 – 1615	21	Potential
	Transmembrane	2363 – 2383	21	Potential
	Domain	1751 – 1917	167	SF3 helicase
	Domain	3155 – 3286	132	RdRp catalytic
	Nucleotide binding	1777 – 1784	8	ATP Potential
	Coiled coil	514 – 604	91	Potential
	Compositional bias	630 – 634	5	Poly-Arg
Sites
	Active site	2680	1	For picornain 3C-like protease activity Probable
	Active site	2722	1	For picornain 3C-like protease activity Probable
	Active site	2811	1	For picornain 3C-like protease activity Probable
	Site	644 – 645	2	Cleavage
	Site	852 – 853	2	Cleavage
	Site	1055 – 1056	2	Cleavage
	Site	2526 – 2527	2	Cleavage Probable
	Site	2852 – 2853	2	Cleavage By similarity
Experimental info
	Mutagenesis	2509	1	Q → R: No effect on processing. Ref.2
	Mutagenesis	2526	1	Q → P: Complete loss of processing between putative helicase and picornain 3C-like protease. Ref.2
	Mutagenesis	2680	1	H → G: Severe loss of polyprotein processing. Ref.3
	Mutagenesis	2717	1	E → Q: Complete loss of polyprotein processing. Ref.3
	Mutagenesis	2735	1	D → E: No effect on polyprotein processing. Ref.3
	Mutagenesis	2811	1	C → A: Complete loss of polyprotein processing. Ref.3
	Mutagenesis	2830	1	H → E: Complete loss of polyprotein processing. Ref.3
	Mutagenesis	2852	1	Q → P: Delayed and partial processing between picornain 3C-like protease and RNA-directed RNA polymerase. Ref.2
	Mutagenesis	2885	1	Q → L: No effect on processing. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Q83034-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: F560A352130E7E96	FASTA	3,473	390,264
	10 20 30 40 50 60 MQSFLLSSKN QAKLLHAGLE FVGGVRCAHQ GWVSGKAVVF CNYCNFAHRL YRFYTKNHCV 70 80 90 100 110 120 LNKELLKISV EGLLCHCIEQ AFLFRRFYDR RFAWQRKYAK GFLFDNLSIP FDDCALCPNA 130 140 150 160 170 180 GTRLSQTGVS HDHFVCNYVE HLFECASFSR ETGGKFFRAC SEGWHWNATC TTCGASCRFA 190 200 210 220 230 240 NPRENIVIAI FMNFLRVMYD GNKYYVSLHC DTEWIPVHPL FARLVLMVRG FAPLDNSHVI 250 260 270 280 290 300 EEDEMDICGH SSEVTYEDPS KFAFTHQHVT RGVGMGHLAF CRDANGVDRG EHKFYLHGPF 310 320 330 340 350 360 DLKMTHAMFR VFMILLNCHG YVQSEFRDEF PDIKDRSLCG LLSVAGLRGV NVSCNEEFIH 370 380 390 400 410 420 LHSQFHNGSF RSQRPIPMVY AEPEMYPPLG YVHLTESWVP RGRLLIDDLP SLMSRVYAES 430 440 450 460 470 480 SQAQAGEIYE ETFDEDDLFE LDGEEGTSTR GLLDLGRRLG GLLLGATKCV KGLHSVIEWP 490 500 510 520 530 540 VDVLTKEAED LGTWLADNKK YVSESTWSCQ VCPEVQDALE KSMREQAKLN AQMISGIKKL 550 560 570 580 590 600 ATTMDSATLK LRDNLKELEQ RISVLEQGAD DTQQVRITNL ENFCEDAAKA FEALRNDIEA 610 620 630 640 650 660 LKKKPAQSVT PLPSPSGNSG TAGEQRPPPR RRRRPPVVEM SEAQAGETVI VGGDEEQEAH 670 680 690 700 710 720 QDSSVAAAGP ADEHNAMLQK IYLGSFKWKV SDGGGSILKT FSLPSDIWAA NDRMKNFLSY 730 740 750 760 770 780 FQYYTCEGMT FTLTITSIGL HGGTLLVAWD ALSSATRRGI VSMIQLSNLP SMTLHASGSS 790 800 810 820 830 840 IGTLTVTSPA IQHQICTSGS EGSLANLGSL VISVANVLCA DSASAQELNV NAWVQFNKPK 850 860 870 880 890 900 LSYWTAQHSI AQSGGFEESQ DLGDLQAIIA TGKWSTTSDK NLMEIIVHPT ACYVSEKLIY 910 920 930 940 950 960 QTNLSVVAHM FAKWSGSMRY TFVFGASMFD RGKIMVSAVP VQFRNSKLTL SQMAAFPSMV 970 980 990 1000 1010 1020 CDLSMETREF TFEVPYISIG KMSLVCKDYL FDISSYNADL VVSRLHVMIL DPLVKTGNAS 1030 1040 1050 1060 1070 1080 NSIGFYVVAG PGKGFKLHQM CGVKSQFAHD VLTAQDFGRS LSCSRLLGNG FKEWCSRESL 1090 1100 1110 1120 1130 1140 LMRVPLKSGK KRAFKYAVTP RMRTLPPEAT SLSWLSQIFV EWRGSLTYTI HVQSGSAIQH 1150 1160 1170 1180 1190 1200 SYMRIWYDPN GKTDEKEVKF LDSAHPPAGI KVYHWDLKIG DSFRFTVPYC ARTEKLQIPK 1210 1220 1230 1240 1250 1260 AYASTPYEWL TMYNGAVTFD LRSGADMELF VSIAGGDDFE MFEQTVPPKC GSVSDSYTVL 1270 1280 1290 1300 1310 1320 SYADDVKSVT EVPNKTTYLA DEQPTTSAPR TSIVNTEDDP PTEGEIARTT NGTLVQYRGG 1330 1340 1350 1360 1370 1380 AWKPMVERTP TMSKKQVGPE LTVSDPQMYK CIKNMNKNVK ILTDRQCTAK LANIVDSAQE 1390 1400 1410 1420 1430 1440 LVGSNSTFVE DLAVGAKQIR KFGESLDVFE GSMSAAKTAE LIDNTHAAFS GPADGSPISN 1450 1460 1470 1480 1490 1500 VVQLLLPMLS SIKGMSGKME SKMASLTAMF QPCKKAITHL IERSFPYLAC KGFKTDKWIW 1510 1520 1530 1540 1550 1560 AALASILVGA ALLHYYRSDL KFVKKWSVMC MIIWAPLLAE KAYHLGTWIK EKFLKSLPRT 1570 1580 1590 1600 1610 1620 RTIKDSCRKH SLAGAFECLA SASCAYIKDN WAKTMSSLLT ILSVVASLVM WGKIPDDKEI 1630 1640 1650 1660 1670 1680 TSFADKFHSI GKKGRSITNI IGGFEKITSV CKKWSETLVS WIVSNVSGGI PKEDLAMTAY 1690 1700 1710 1720 1730 1740 LGFKIHDWVR ETRDMALMEN RFRGFGGDEH LVKVRRLYGH SLKIDNALME KQIVPDMQLS 1750 1760 1770 1780 1790 1800 LIIKECRQKC LELMNESYTY KGMKQSRIDP LHVCMLGAPG VGKSTIAHVV INHLLDHRGE 1810 1820 1830 1840 1850 1860 PEVDRIYTRS CADAYWSNYH QEPVILYDDL GAIKSNLRLS DYAEIMGIKT NDPFSVPMAA 1870 1880 1890 1900 1910 1920 VEDKGKHCTS KYVFSCTNVL NLDDTGDVVT KMAYYRRRNV LVKVERDPDV PKNEANPTEG 1930 1940 1950 1960 1970 1980 LVFTVLGHDQ NCQGDPQFVV KENWDEPFLR EVDTEGWRFE RVEYRTFLRF LCMYTDAYMY 1990 2000 2010 2020 2030 2040 SQEQVLQGIK TFKMNPFAPE PEFAQAQNGE AAECEIVEEM QEVPGEAPQE AKELVKIETA 2050 2060 2070 2080 2090 2100 PNMDELVEAF NKLRVTPGHL NDILRDGSGC YIDEWAIAGP RWLSFHELLP FTCGCHHTRV 2110 2120 2130 2140 2150 2160 CDFNIVYNNM CKAVRSQSVH FKYRANQAIK YAYTHKLHSQ CRYSIDFEKL RECNPLDVFV 2170 2180 2190 2200 2210 2220 CVLSKYTADD HSFERRCPKK MNVVRMQRPP VFELKMRPPS DSVVVEDEQG QRIFEWPHLY 2230 2240 2250 2260 2270 2280 IFLRYRAIEF KDDKGSLTVR EDAGADVCPW NEFLKLPWLD GDQLKSVLPA HLHRMVQARL 2290 2300 2310 2320 2330 2340 EQVEIMEENG NYSGEMRNAI AEIKEYLDQD HQWVAALVLV ACAVKERRRM THDKLHRKSF 2350 2360 2370 2380 2390 2400 NALDKLDAWY TTTAPKTSKK MKILLAIGAS VAVAGVAVGA VILLQKTNLF GSKEDEEIEG 2410 2420 2430 2440 2450 2460 EEGETQASGA HESDGIVTQH LKRDIRPKMR VTYTDHHVAE AHEEKDAEKP RKSGNPTRKS 2470 2480 2490 2500 2510 2520 YLGLSPGFAE RGMGVTYEEH TPLKDALLDE SNKVFRRKIV ASVESAVKQG GKASKDTVLS 2530 2540 2550 2560 2570 2580 QIGDWQDKVK ATGVIAARQL EASGSLKKIH NLNSRRTSSH VMPGLVVHDG AFERSDEVDA 2590 2600 2610 2620 2630 2640 ELHRITIDEV KSCPKMIKEG VSTLSVKKAS VGMLALQKAE SQLSFPFTSR AGVDRDLSMT 2650 2660 2670 2680 2690 2700 NLIDTHMAGM SCIIISELGN VFRTFGVLRL CGTYVCMPAH YLDEITSEHT LYFVCPSKIT 2710 2720 2730 2740 2750 2760 QIQLERHRVC LVNGFQETVV WDLGPSVPPS RNYIDFIANA DDWKNYKATS GALVMSKYSV 2770 2780 2790 2800 2810 2820 DSMLQCVHFL DSIELTEANV SVPTSYYEAN GGIHTIISGL RYRVHCMPGF CGRAIMRADA 2830 2840 2850 2860 2870 2880 TCFRKIIGMH VSGLRNKCMG YAETLTQEHL MQAIETLKET GLLKHIPKGA IGAGEEKLPE 2890 2900 2910 2920 2930 2940 HSKKQSLSLE GKGNLGIVGQ LTAQLVPTSV TKTTICKSMI HGLIGEIKTE PSVLSAWDRR 2950 2960 2970 2980 2990 3000 LPFPPGEWDP MKDAVKKYGS YILPFPTEEI QEVENFLIKK FRRKENSRRT RNVNSLEVGI 3010 3020 3030 3040 3050 3060 NGIDGSDFWS PIEMKTSPGY PYILKRPSGA QGKKYLFEEL EPYPSGRPKY AMKDPELIEN 3070 3080 3090 3100 3110 3120 YERIKEEVTS GVKPSIMTME CLKDERRKLA KIYEKPATRT FTILSPEVNI LFRQYFGDFA 3130 3140 3150 3160 3170 3180 AMVMSTRREH FSQVGINPES MEWSDLINSL LRVNTKGFAG DYSKFDGIGS PAIYHSIVNV 3190 3200 3210 3220 3230 3240 VNAWYNDGEV NARARHSLIS SIVHRDGICG DLILRYSQGM PSGFAMTVIF NSFVNYYFMA 3250 3260 3270 3280 3290 3300 LAWMSTVGSS LLSPQGSCKD FDTYCKIVAY GDDNVVSVHE EFLDVYNLQT VAAYLSHFGV 3310 3320 3330 3340 3350 3360 TYTDGDKNPI HMSKPYEDIT KMSFLKRGFE RVESSGFLWK APLDKTSIEE RLNWIRDCPT 3370 3380 3390 3400 3410 3420 PVEALEQNIE SALHEAAIHG RDYFDDLVRR LNSALTRVML PPTDISFEEC QARWWASVTG 3430 3440 3450 3460 3470 ALRAADYTSL VRRASSGHVE FNKKYRDMFR QQDLPLKEIL MKSKPVALLD LEV

References

[1]	"Nucleotide sequence and genomic organization of rice tungro spherical virus." Shen P., Kaniewska M., Smith C., Beachy R.N. Virology 193:621-630(1993) [PubMed: 8460478] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], PROTEIN SEQUENCE OF 645-659; 853-867 AND 1056-1073, PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[2]	"Rice tungro spherical virus polyprotein processing: identification of a virus-encoded protease and mutational analysis of putative cleavage sites." Thole V., Hull R. Virology 247:106-114(1998) [PubMed: 9683576] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN, MUTAGENESIS OF GLN-2509; GLN-2526; GLN-2526; GLN-2852 AND GLN-2885.
[3]	"Characterization of a protein from Rice tungro spherical virus with serine proteinase-like activity." Thole V., Hull R. J. Gen. Virol. 83:3179-3186(2002) [PubMed: 12466496] [Abstract] Cited for: CHARACTERIZATION OF PICORNAIN 3C-LIKE PROTEASE, MUTAGENESIS OF HIS-2680; GLU-2717; ASP-2735; CYS-2811 AND HIS-2830.

Cross-references

Sequence databases
EMBLGenBankDDBJ	M95497 Genomic RNA. Translation: AAA66056.1.
PIR	A46112. S27927.
RefSeq	NP_042507.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	1497257.
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_RTSVA

Accession

Primary (citable) accession number: Q83034

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 30, 2005
Last sequence update:	November 1, 1996
Last modified:	June 16, 2009
This is version 55 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)