Reviewed, UniProtKB/Swiss-Prot Q8JJX1 (POLN_SPDV)

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	Salmon pancreas disease virus (SPDV)
Taxonomic identifier	84589 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus
Virus host	Salmo salar (Atlantic salmon) [TaxID: 8030]

Protein attributes

Sequence length	2601 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	Host cell membrane Host cytoplasm Host endosome Host lysosome Host membrane Host nucleus Membrane
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	extrinsic to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
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 methyltransferase activity Inferred from electronic annotation. Source: UniProtKB-KW 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 – 2601	2601	Non-structural polyprotein		PRO_0000308407
	Chain	1 – 1992	1992	P123 By similarity		PRO_0000228796
	Chain	1 – 562	562	mRNA-capping enzyme nsP1 By similarity		PRO_0000228797
	Chain	563 – 1421	859	Protease/triphosphatase/NTPase/helicase nsP2 By similarity		PRO_0000228798
	Chain	1422 – 1992	571	Non-structural protein 3 By similarity		PRO_0000228799
	Chain	1993 – 2601	609	RNA-directed RNA polymerase nsP4 By similarity		PRO_0000228800
Regions
	Domain	994 – 1199	206	Peptidase C9
	Domain	1422 – 1581	160	Macro
	Domain	2357 – 2472	116	RdRp catalytic
	Nucleotide binding	751 – 758	8	ATP Potential
	Region	260 – 279	20	nsP1 membrane-binding By similarity
	Region	1035 – 1055	21	Nucleolus localization signal By similarity
	Motif	1219 – 1223	5	Nuclear localization signal By similarity
Sites
	Active site	1044	1	For cysteine protease nsP2 activity By similarity
	Active site	1114	1	For cysteine protease nsP2 activity By similarity
	Site	562 – 563	2	Cleavage; by nsP2 By similarity
	Site	1421 – 1422	2	Cleavage; by nsP2 By similarity
	Site	1992 – 1993	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)
	Q8JJX1-1 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: B052C737954909BE	FASTA	2,601	285,752
	10 20 30 40 50 60 MMQNLTANPS AGATVTVNLP ADHPALNQFK TAFPGFEVVA SNRSSNDHAA ARAFSHLATK 70 80 90 100 110 120 WIERDIGGRQ VIVADIGSAP ARRIGAPDNV TYHSVCPRKC AEDPERLASY ARKLVRAVER 130 140 150 160 170 180 GDGHLVNEKI 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 GIVGIPAKEE LATSYHRDGV VVTKFSDTIN HEQVSFPVVT YIPAVICDQM 370 380 390 400 410 420 TAMTANPVKY SDAVKLLVGL NQRIVVNGTT VRNVNSMDNS LIPVFARALC SWADEVRRDM 430 440 450 460 470 480 EDEQDLYGIT SVTTWICICR AYDKRQQHTF YRRPKQSSGI YVPAKFTGSL RAALSATYLN 490 500 510 520 530 540 LPLKQLLLNT LKRAIKPMDQ AIADETEALA HDAAEVHELT EEERRQQAAN PSYIADVLGQ 550 560 570 580 590 600 DDDEEEAGDG MSDVDLGEED GAGATIIDCQ RGTVKVITAF GDNMMGEYLV LSPVTVLRTR 610 620 630 640 650 660 KLAILLGPLA EEVMQYVHKG RTGRYAIEKN NLKVLIPTGV SLKTDHFQAL AESATLTYND 670 680 690 700 710 720 YLFTCRTLDQ LATRGSARNT DEVYYKLVDA AKARDEYVYE LSSKQCVKKE DATGTVLQGD 730 740 750 760 770 780 ICNPPYHQFA YEALRKRPAH THDVHTIGIY GVPGAGKTAI ITTEVTTRDL VASGKKENCE 790 800 810 820 830 840 DIKRCVLERR GLKIAARTVD SLFYGAYRGA VNTLYVDEAY ACHSGTLLAL IAAVRPTGKV 850 860 870 880 890 900 VLCGDPKQVG CVNQLQMRMH YNHEISDRVL RKNISRRCTH TLTAIVSNLN YEGRMKTTNP 910 920 930 940 950 960 CKKPVLIDTT GSTKPDKEAL VLTCFRGWVK DLKFLYPHNE LMTAAASQGL TREKVYAVRC 970 980 990 1000 1010 1020 RVTTNPLYEP TSEHITVLLT RTNDELVWKT LPNDPLIPIL SKPPKGDYSA TMEDWEDEHN 1030 1040 1050 1060 1070 1080 GILAALREAC VPRMNFAHGK RNTCWAVTSS RVLHEAGVQI TPEDYNRIFP AFREDKPHSA 1090 1100 1110 1120 1130 1140 LAALDAVATL VWGLDTSSGI LSGKGSFMRL ENSHWSNSNR GYEYGLNLDA LEGYEIANPR 1150 1160 1170 1180 1190 1200 MIKALKQRRG RECYDIETGK LVPLDPARVQ VPINRIVPHV LVDTSAAAKP GFLENRLTVD 1210 1220 1230 1240 1250 1260 RWDQVHSFKT RAAVKFAELT KRVSYNSVLD LGAAPGGVTD YCVKKGKTVT SVSEQWDTKP 1270 1280 1290 1300 1310 1320 RGAVVVTADI NGPLNNLGIF DLVFCDAAGP RRYHHYAQCE DHAVLFTSAC KHGVERTAKG 1330 1340 1350 1360 1370 1380 GVFIVKAYGM ADRRTERAVE GTARYFRSVS VEKPVSSRIT NVEVFFKFSG RCRPHARSIA 1390 1400 1410 1420 1430 1440 HLGPQLTDIY ARTWKAYKML ARGSVADKVK VAEILNSMVG AAPGYRVLNR NIITAEEEVL 1450 1460 1470 1480 1490 1500 VNAANSNGRP GDGVCGALYG AFGDAFPNGA IGAGNAVLVR GLEATIIHAA GADFREVDEE 1510 1520 1530 1540 1550 1560 TGARQLRAAY RAAATLVTAN GITSAAIPLL STHIFSNGRN RLEQSFSALV EAFDTTECDV 1570 1580 1590 1600 1610 1620 TIYCLANNMA ARIQQLIDAH AREEFDEEVV VEEEEEHEAD AMSDTETLSS FGDETVWVPK 1630 1640 1650 1660 1670 1680 HSTLAGRPGY SAYYGDRRSL FVGTKFHRAA VAMSSIEAAW PKTKEANAKL IEYIRGQHLV 1690 1700 1710 1720 1730 1740 DVLKSCPVDD IPVGRPPSSL PCGCIYAMTP ERVTVLKQRP QEGFVVCSAF KLPLTNIQDV 1750 1760 1770 1780 1790 1800 TKVECTVRAP AEEPRPVRHL QERRPAQAAV RQLRPAAVAA SVAASHTASR TSTASSRRTP 1810 1820 1830 1840 1850 1860 APGSVQVRLL PPRDGTESRS SRMGSQSSVT SSAGSVPPAP RRAPAVSAAS LASSAHSRSV 1870 1880 1890 1900 1910 1920 RSAPAMRAAS AGARSVRSAQ SGSTGHRAGA FSVAGSVRQP SGPPSSVSTP AAIRGLTRDQ 1930 1940 1950 1960 1970 1980 FDAVRVRARR NLELEGSEHG SQSSFHSGSL AVGSSASSYS QRSDDQDTGT EPSSRGAAVR 1990 2000 2010 2020 2030 2040 TRRRGQRDGL GGYIFSSDQG TAHLSQHNTQ TNNTTEVLMR TSVLPSNDHG TPDLPAETRK 2050 2060 2070 2080 2090 2100 RLAYQMRPTQ KNKSRYLSAK VHNMKHKIVR CLQRGAGHYL REQHALPLWK NTFPKPRYSD 2110 2120 2130 2140 2150 2160 ACVVKFESVN TAIVAANMFI GCNYPTLSSF GITDKYDAYL DMVDGLNCNL DTVTFDPAKV 2170 2180 2190 2200 2210 2220 RSLPKKSEYN QPLIQSQVPG PMTSTLQSIL MAATKRNCNV TQMRELPTMD SAAMNVEAFK 2230 2240 2250 2260 2270 2280 SFACKDTDLW TEFAEKPVRL SPGQIEEYVF HLQGAKANVM HSRVEAVCPD LSEVAMDRFT 2290 2300 2310 2320 2330 2340 LDMKRDVKVT PGTKHVEERP KVQEIQAADP MATAYLCAIH RELVRRLKAV LKPSIHVLFD 2350 2360 2370 2380 2390 2400 MSSEDFDAIV GHGMKLGDKV LETDISSFDK SQDQAMAVTA LMLLRDLGVE EDLLTLIEAS 2410 2420 2430 2440 2450 2460 FGDITSAHLP TGTRFQFGSM MKSGLFLTLF VNTLLNITIA ARVLREQLAD TRCAAFIGDD 2470 2480 2490 2500 2510 2520 NVITGVVSDD MMVARCASWL NMEVKIMDME IGNMSPYFCG GFLLLDTVTG TVSRVSDPVK 2530 2540 2550 2560 2570 2580 RLMKMGKPAL NDPETDVDRC RALREEVESW YRVGIQWPLQ VAAATRYGVN HLPLATMAMA 2590 2600 TLAQDLRSYL GARGEYVSLY V

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
EMBL GenBank DDBJ	AJ316244 Genomic RNA. Translation: CAC87721.1.
RefSeq	NP_647496.1.
3D structure databases
SMR	Q8JJX1. Positions 810-898, 1038-1393, 1423-1553, 2299-2464.
ModBase	Search...
Genome annotation databases
GeneID	2193531.
Enzyme and pathway databases
BRENDA	2.7.7.48. 297069. 3.1.3.33. 297069. 3.6.1.15. 297069.
Family and domain databases
InterPro	IPR002589. A1pp. IPR002620. Peptidase_C9. IPR001788. RNA-dep_RNA_pol_vir-typ. IPR007094. RNA-dir_pol_PSvirus. 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. [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_SPDV

Accession

Primary (citable) accession number: Q8JJX1

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 21, 2006
Last sequence update:	October 1, 2002
Last modified:	February 9, 2010
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)