Reviewed, UniProtKB/Swiss-Prot Q8QL53 (POLN_SLDV)

Names and origin

Protein names	Recommended name:     Non-structural polyprotein Alternative name(s):     Polyprotein nsP1234       Short name=P1234 Cleaved into the following 5 chains:     1- Recommended name:             P123     2- Recommended name:             mRNA-capping enzyme nsP1               EC=2.1.1.-               EC=2.7.7.-         Alternative name(s):             Non-structural protein 1     3- Recommended name:             Protease/triphosphatase/NTPase/helicase nsP2               EC=3.4.22.-               EC=3.1.3.33               EC=3.6.1.15               EC=3.6.1.-         Alternative name(s):             Non-structural protein 2               Short name=nsP2     4- Recommended name:             Non-structural protein 3                 Short name=nsP3     5- Recommended name:             RNA-directed RNA polymerase nsP4               EC=2.7.7.48         Alternative name(s):             Non-structural protein 4               Short name=nsP4
Organism	Sleeping disease virus (SDV)
Taxonomic identifier	78540 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus
Virus host	Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) [TaxID: 8022]

Protein attributes

Sequence length	2593 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	P123 is short-lived polyproteins, accumulating during early stage of infection. It localizes the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, it starts viral genome replication into antigenome. After these early events, P123 is cleaved sequentially into nsP1, nsP2 and nsP3. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex By similarity. nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell By similarity. nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins By similarity. nsP3 is essential for minus strand and subgenomic 26S mRNA synthesis By similarity. nsP4 is a RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA encodes for structural proteins By similarity.
Catalytic activity	S-adenosyl-L-methionine + GTP = m7GTP. m7GTP + (5')pp-Pur-mRNA = diphosphate + m7G(5')ppp-Pur-mRNA. (5')ppp-mRNA + H2O = (5')pp-mRNA + phosphate. A 5'-phosphopolynucleotide + H2O = a polynucleotide + phosphate. NTP + H2O = NDP + phosphate. Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subunit structure	P123 interacts with nsP4; nsP1, nsP2, nsP3 and nsP4 interact with each other, and with uncharacterized host factors.
Subcellular location	Non-structural polyprotein: Host endosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host lysosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Note: Located on the cytoplasmic surface of modified endosomes and lysosomes, also called cytopathic vacuoles type I (CPVI). These vacuoles contain numerous small circular invaginations (spherules) which may be the sites of RNA synthesis. P123: Host endosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host lysosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. mRNA-capping enzyme nsP1: Host endosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host lysosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host cell membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Note: In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then a fraction of nsP1 localizes to the inner surface of the plasma membrane By similarity. Protease/triphosphatase/NTPase/helicase nsP2: Host endosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host lysosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host nucleus By similarity. Note: In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then approximately half of nsP2 is found in the nucleus By similarity. Non-structural protein 3: Host endosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host lysosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host cytoplasm By similarity. Note: In the late phase of infection, the polyprotein is quickly cleaved before localization to cellular membranes. Then nsP3 and nsP3' seems to aggregate in cytoplasm By similarity. RNA-directed RNA polymerase nsP4: Host endosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host lysosome membrane; Peripheral membrane protein; Cytoplasmic side By similarity.
Induction	Viral replication produces dsRNA in the late phsae of infection, resulting in a strong activation of host EIF2AK2/PKR, leading to almost complete phosphorylation of EIF2A. This inactivates completely cellular translation initiation, resulting in a dramatic shutoff of proteins synthesis. Translation of viral non-structural polyprotein and all cellular proteins are stopped in infected cell between 2 and 4 hours post infection. Only the 26S mRNA is still translated into viral structural proteins, presumably through a unique mechanism of enhancer element which counteract the translation inhibition mediated by EIF2A. By doing this, the virus uses the cellular defense for its own advantage: shutoff of cellular translation allows to produce big amounts of structural proteins needed for the virus to bud out of the doomed cell.
Post-translational modification	Specific enzymatic cleavages in vivo yield mature proteins. The polyprotein is synthesized as P1234 by stop codon readthrough. This polyprotein is processed differently depending on the stage of infection. In early stages, P1234 is first cleaved in trans, through its nsP2 protease activity, releasing P123 and nsP4. P123 and nsP4 start to replicate the viral genome into its antigenome. After these early events, nsP1 is cleaved in cis by nsP2 protease, releasing P23 polyprotein. Cleavage of nsP1 exposes an 'activator' at the N-terminus of P23 which induces its cleavage into nsP2 and nsP3 by the viral protease. This sequence of delayed processing would allow correct assembly and membrane association of the RNA-polymerase complex. In the late stage of infection, the presence of free nsP2 in the cytoplasm cleaves P1234 quickly into P12 and P34, then into the four nsP By similarity. nsP1 is palmitoylated by host By similarity. nsP3 is phosphorylated by host on serines and threonines By similarity. nsP4 is ubiquitinated; targets the protein for rapid degradation via the ubiquitin system By similarity.
Sequence similarities	Contains 1 Macro domain. Contains 1 peptidase C9 domain. Contains 1 RdRp catalytic domain.
Caution	There is no stop codon readthrough before nsp4.

Ontologies

Keywords
Biological process	RNA replication mRNA capping mRNA processing
Cellular component	Cell membrane Cytoplasm Endosome Lysosome Membrane Nucleus
Ligand	ATP-binding GTP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase Methyltransferase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
PTM	Lipoprotein Palmitate Ubl conjugation
Technical term	Multifunctional enzyme
Gene Ontology (GO)
Biological process	mRNA capping Inferred from electronic annotation. Source: UniProtKB-KW methylation 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	endosome Inferred from electronic annotation. Source: UniProtKB-KW host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell host cell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell lysosome Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW GTP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA helicase activity 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 mRNA methyltransferase activity Inferred from electronic annotation. Source: InterPro polynucleotide 5'-phosphatase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 2593	2593	Non-structural polyprotein		PRO_0000308406
	Chain	1 – 1984	1984	P123 By similarity		PRO_0000228791
	Chain	1 – 561	561	mRNA-capping enzyme nsP1 By similarity		PRO_0000228792
	Chain	562 – 1420	859	Protease/triphosphatase/NTPase/helicase nsP2 By similarity		PRO_0000228793
	Chain	1421 – 1984	564	Non-structural protein 3 By similarity		PRO_0000228794
	Chain	1985 – 2593	609	RNA-directed RNA polymerase nsP4 By similarity		PRO_0000228795
Regions
	Domain	993 – 1198	206	Peptidase C9
	Domain	1421 – 1580	160	Macro
	Domain	2349 – 2464	116	RdRp catalytic
	Nucleotide binding	750 – 757	8	ATP Potential
	Region	260 – 279	20	nsP1 membrane-binding By similarity
	Region	1034 – 1054	21	Nucleolus localization signal By similarity
	Motif	1218 – 1222	5	Nuclear localization signal By similarity
Sites
	Active site	1043	1	For cysteine protease nsP2 activity By similarity
	Active site	1113	1	For cysteine protease nsP2 activity By similarity
	Site	561 – 562	2	Cleavage; by nsP2 By similarity
	Site	1420 – 1421	2	Cleavage; by nsP2 By similarity
	Site	1984 – 1985	2	Cleavage; by nsP2 By similarity
Amino acid modifications
	Lipidation	437	1	S-palmitoyl cysteine; by host By similarity
	Lipidation	439	1	S-palmitoyl cysteine; by host By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q8QL53-1 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: 2E2B4F651A45B8CF	FASTA	2,593	284,853
	10 20 30 40 50 60 MMLNLTANPS AGTTVTVDLP ADHPALNQFK TAFPGFEVVA SNRSSNDHAA ARAFSHLATK 70 80 90 100 110 120 WIERDIDGRQ VIVADIGSAP ARRVGAPDNV TYHSVCPRKC AEDPERLASY ARKLVRAVEK 130 140 150 160 170 180 GDGHLVSDRI TDLKDVLENP DTSLETTSIC LNDDVSCKVK ADIAVYQDVY AVDAPSTIYA 190 200 210 220 230 240 QADKGTRVVY WIGFEPFVFH TDAMAGSFPL YDANWSDSAV LAAKNLPLCY SGLSEDSIKW 250 260 270 280 290 300 RFRFRDKPLV PSGEIHYSVG STHYVEDRDK LKSWHLPSTF HFVAPNKYTC RCDTVVSCGG 310 320 330 340 350 360 YVVKKITICE GIVGRPANEE LATSYHRDGV VVTKFSDTIN HEQVSFPVVT YIPAVICDQM 370 380 390 400 410 420 TAMTADPVKY PDVVKLLVGL NQRIVVNGTT VRNVNSMDNS LIPVFARALC SWADEARRDM 430 440 450 460 470 480 EDEQDMYGVT SVTTWICICR AYDKRQQHTF YRRPKQSSGI YVPAKFTGSL RASLSATYLN 490 500 510 520 530 540 LPLKQLLLNT LKRAIKPGDQ ALADETEARA HDAAEVHELT EEEGRQQAAN PSYIADVLGQ 550 560 570 580 590 600 DDEEEVDDGM SNVDLGEEDG VGSTIIDCQR GTVKVITAFG DNTMGEYLVL SPVTVLRTRK 610 620 630 640 650 660 LAVLLGPLAE EVMQYVHKGR TGRYAIEKNN LKVLIPTGVS LKTAHFQALT ESATLTYNDY 670 680 690 700 710 720 LFTCRTLDQL ATRGSAKNTD EVYYKLVDAA KAKDEYVYEL SSKQCVKKED ATGTVLQGDI 730 740 750 760 770 780 CNPPYHQFAF EALRKRPAHT HDVHTIGIYG VPGAGKTAII TTEVTTRDLV ASGKKENCED 790 800 810 820 830 840 IKRCVLERRG LKIAARTVDS LLYGAYRGAV DTLYVDEAYA CHSGTLLALI AAVRPTGKVV 850 860 870 880 890 900 LCGDPKQVGC VNQLQMRMHY NHEISDRVLR KNISRRCTHT LTAIVSNLNY EGRMKTTNPC 910 920 930 940 950 960 KKPVLIDTTG STKPDKEALV LTCFRGWVKD LKILYPHNEL MTAAASQGLT REKVYAVRCR 970 980 990 1000 1010 1020 VTSNPLYEPT SEHITVLLTR TNDELVWKTL PNDPLIPILS KPPKGDYSAT MEDWEDEHNG 1030 1040 1050 1060 1070 1080 ILAALREACV PRMNFAHGKR NTCWAVTSSR VLHEAGVLIT PEDFNRIFPA FREDKPHSAL 1090 1100 1110 1120 1130 1140 AALDAVAALV WGLDTSSGIL SGKGSFMRLE NSHWSNSNRG YEYGLNLDAL EGYEIANPRM 1150 1160 1170 1180 1190 1200 IKALKQRRGR ECYDIETGKL VPMDPGRVQV PINRVVPHVL VDTSAAAKPG FLENRLSVDR 1210 1220 1230 1240 1250 1260 WDQVHSFKTR AAVKFAELTK RVSYNSVLDL GAARGGVTDY CVKKGKTVTC VSEQWDSKPR 1270 1280 1290 1300 1310 1320 GAVVITADIN GPLNNLGIFD LVFCDAAGPR RYHHYAQCED HARRSTSACK HGVERTAKGG 1330 1340 1350 1360 1370 1380 VFIVKAYGMA DRRTERAVEC TARYFKSVSV EKPVSSRITN VEVFFKFSGR CRPHARSIAH 1390 1400 1410 1420 1430 1440 LGPQLTDIYA RTRKAYKMLA RGSVADKVKV AEILNSMVGA APGYRVLNKN IITAEEEVLV 1450 1460 1470 1480 1490 1500 NAANSNGRPG DGVCGALYGA FGDAFPNGAI GAGNAVLVRG LEATIIHAAG ADFREVDEET 1510 1520 1530 1540 1550 1560 GARQLRAAYR AAATLVTANG ITSAAIPLLS THIFSNGRNR LEQSFGALVE AFDTTECDVT 1570 1580 1590 1600 1610 1620 IYCLANNMAA RIQQLIDDHA REEFDEEVVV EEEEEHEANA MCDTETLSSF GDETVWVPKH 1630 1640 1650 1660 1670 1680 STLAGRPGYS ATYGDRRSLF VGTKFHRAAV AMSSIEAAWP RTKEANAKLI EYIRGQHLVD 1690 1700 1710 1720 1730 1740 VLKSCPVNDI PVGRPPSSLP CGCIYAMTPE RVTVLKQRPQ EGFVVCSAFK LPLTNIQDVT 1750 1760 1770 1780 1790 1800 KVECTVRAPA EEPRPVRYLQ ERRPVQAAAR QPRPAIVAAS VAGTATSRRT PAPGSVQVRL 1810 1820 1830 1840 1850 1860 LPPRDGTVSR SSRTSSQSSV TSSAGPIMPV PRRAPVAPAA SLAGSVHSHS VRSAPAILRA 1870 1880 1890 1900 1910 1920 ASTGARSVRS VQSGLTGHRD DAVSVAGSVR QPSGPPSSVS TPAAPRGLTR EQFGAVRARA 1930 1940 1950 1960 1970 1980 RRDLELEGSE HGSQASFRSG SLVVGSTASS YSQRPDDQDT GSEPSGRGAA VRTRRRGQRD 1990 2000 2010 2020 2030 2040 GPGGYIFSSD QGTAHLSQHN TQTNNTTEVL MRTSVLPSND HGTPDLLAEM KKRLAYQMRP 2050 2060 2070 2080 2090 2100 TQKNKSRYLS AKVHNMKHKI VQCLQRGAGH YLREQHALPL WKNTFPKPRY SDACVVKFES 2110 2120 2130 2140 2150 2160 VNTAIVAANM FIGCNYPTLS SFGVTDKYDA YLDMVDGLNC NLDTVTFEPA KVRSLPKKSK 2170 2180 2190 2200 2210 2220 YNQPLIQSQV PGPMASTLQS ILMAATKRNC NVTQMRELPT MDSAAMNVEA FKKFACKDTD 2230 2240 2250 2260 2270 2280 LWTEFAEKPV RLSPGQIEEY VFHLQGAKAN VMHSRVEAAC PDLSEVAMDR FTLDMKRDVK 2290 2300 2310 2320 2330 2340 VTPGTKHVEE RPKVQVIQAA DPMATAYLCA IHRELVRRLK AVLKPSIHVL FDMSSEDFDA 2350 2360 2370 2380 2390 2400 IVGHGMKLGD KVLETDISSF DKSQDQAMAV TALMLLEDLG VEEDLLTLIE ASFGDITSVH 2410 2420 2430 2440 2450 2460 LPTGTRFQFG SMMKSGLFLT LFVNTLLNIT IAARVLREQL ADTRCAAFIG DDNVITGVVS 2470 2480 2490 2500 2510 2520 DDMMVARCAS WLNMEVKIME MEIGDRSPYF CGGFLLLDTV TGTVSRVSDP VKRLMKMGKP 2530 2540 2550 2560 2570 2580 ALNDPETDVD RCRALREEVE SWYRVGIQWP LQVAAATRYG VNHLPLATMA MATLAQDLRS 2590 YLGARGEYVS LYA

References

[1]

"Comparison of two aquatic alphaviruses, Salmon pancreas disease virus and Sleeping disease virus, by using genome sequence analysis, monoclonal reactivity and cross-infection." Weston J.H., Villoing S., Bremont M., Castric J., Pfeffer M., Jewhurst V., McLoughlin M., Rodseth O., Christie K.E., Koumans J., Todd D. J. Virol. 76:6155-6163(2002) [PubMed: 12021349] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AJ316246 Genomic RNA. Translation: CAC87660.1.
RefSeq	NP_598184.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	1729819.
Enzyme and pathway databases
BRENDA	2.7.7.48. 301707. 3.1.3.33. 301707. 3.6.1.15. 301707.
Family and domain databases
InterPro	IPR002589. A1pp. IPR002588. MeTrfase_vir. IPR002620. Peptidase_C9. IPR001788. RNA-dep_RNA_pol_vir-typ. IPR000606. RNA_helicase1_vir. IPR007094. RNA_pol_PSvir. IPR002877. rRNA_MeTrfase_RrmJ/FtsJ. [Graphical view]
Pfam	PF01728. FtsJ. 1 hit. PF01661. Macro. 1 hit. PF01707. Peptidase_C9. 1 hit. PF00978. RdRP_2. 1 hit. PF01443. Viral_helicase1. 1 hit. PF01660. Vmethyltransf. 1 hit. [Graphical view]
SMART	SM00506. A1pp. 1 hit. [Graphical view]
PROSITE	PS51154. MACRO. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLN_SLDV

Accession

Primary (citable) accession number: Q8QL53

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 21, 2006
Last sequence update:	June 1, 2002
Last modified:	June 16, 2009
This is version 48 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)