Reviewed, UniProtKB/Swiss-Prot O90368 (POLN_ONNVS)

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	O'nyong-nyong virus (strain SG650) (ONNV)
Taxonomic identifier	374989 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus › SFV complex
Virus host	Homo sapiens (Human) [TaxID: 9606] Anopheles [TaxID: 44482]

Protein attributes

Sequence length	2513 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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 = m(7)GTP. m(7)GTP + (5')pp-Pur-mRNA = diphosphate + m(7)G(5')ppp-Pur-mRNA. (5')ppp-mRNA + H(2)O = (5')pp-mRNA + phosphate. A 5'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate. NTP + H(2)O = 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 By similarity.
Subcellular location	Non-structural polyprotein: Endosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. Lysosome membrane; Peripheral membrane protein; Cytoplasmic sideBy 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: Endosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. Lysosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. mRNA-capping enzyme nsP1: Endosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. Lysosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. Cell membrane; Peripheral membrane protein; Cytoplasmic sideBy 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: Endosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. Lysosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. NucleusBy 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: Endosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. Lysosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. CytoplasmBy 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: Endosome membrane; Peripheral membrane protein; Cytoplasmic sideBy similarity. Lysosome membrane; Peripheral membrane protein; Cytoplasmic sideBy 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. nsP4 is ubiquitinated; targets the protein for rapid degradation via the ubiquitin system By similarity.
Sequence similarities	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 Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase Methyltransferase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
PTM	Lipoprotein Palmitate Phosphoprotein Ubl conjugation
Technical term	Multifunctional enzyme
Gene Ontology (GO)
Biological process	mRNA capping Inferred from electronic annotation. Source: UniProtKB-KW 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 lysosomal membrane Inferred from electronic annotation. Source: UniProtKB-SubCell 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 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: InterPro 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 – 2513	2513	Non-structural polyprotein		PRO_0000308399
	Chain	1 – 1902	1902	P123 By similarity		PRO_0000229938
	Chain	1 – 535	535	mRNA-capping enzyme nsP1 By similarity		PRO_0000229939
	Chain	536 – 1333	798	Protease/triphosphatase/NTPase/helicase nsP2 By similarity		PRO_0000229940
	Chain	1334 – 1902	569	Non-structural protein 3 By similarity		PRO_0000229941
	Chain	1903 – 2513	611	RNA-directed RNA polymerase nsP4 By similarity		PRO_0000229942
Regions
	Domain	964 – 1165	202	Peptidase C9
	Domain	2267 – 2382	116	RdRp catalytic
	Nucleotide binding	721 – 728	8	ATP Potential
	Region	244 – 263	20	nsP1 membrane-binding By similarity
	Region	1005 – 1024	20	Nucleolus localization signal By similarity
	Motif	1182 – 1186	5	Nuclear localization signal By similarity
Sites
	Active site	1013	1	For cysteine protease nsP2 activity By similarity
	Active site	1083	1	For cysteine protease nsP2 activity By similarity
	Site	535 – 536	2	Cleavage; by nsP2 By similarity
	Site	1333 – 1334	2	Cleavage; by nsP2 By similarity
	Site	1902 – 1903	2	Cleavage; by nsP2 By similarity
Amino acid modifications
	Lipidation	417	1	S-palmitoyl cysteine; by host By similarity
	Lipidation	419	1	S-palmitoyl cysteine; by host By similarity

Sequences

	Sequence		Length	Mass (Da)
	O90368-1 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: 1B546AD981E5F2A7	FASTA	2,513	280,222
	10 20 30 40 50 60 MDSVYVDIDA DSAFLKALQR AYPMFEVEPK QVTPNDHANA RAFSHLAIKL IEQEIDPDST 70 80 90 100 110 120 ILDIGPAPAR RMMSDRKYHC VCPMRSAEDP ERLANYARKL ASAAGKVTDK NISGKINDLQ 130 140 150 160 170 180 AVMAVPNMET STFCLHTDAT CKQRGDVAIY QDVYAVHAPT SLYHQAIKGV RVAYWIGFDT 190 200 210 220 230 240 TPFMYNAMAG AYPSYSTNWA DEQVLKAKNI GLCSTDLSEG RRGKLSIMRG KKLKPCDRVL 250 260 270 280 290 300 FSVGSTLYPE SRKLLQSWHL PSVFHLKGKL SFTCRCDTIV SCEGYVVKRV TMSPGIYGKT 310 320 330 340 350 360 SGYAVTHHAD GFLMCKTTDT VDGERVSFSV CTYVPATICD QMTGILATEV TPEDAQKLLV 370 380 390 400 410 420 GLNQRIVVNG RTQRNTNTMK NYLLPIVAQA FSKWAKECRK DMEDEKLLGV RERTLTCCCL 430 440 450 460 470 480 WAFRKHKTHT VYKRPDTQSI QKVPAEFDSF VIPSLWSSGL SIPLRTRIKW LLSKAPKHEQ 490 500 510 520 530 540 LPHSGNAEEA AQAEMDAAEE REAELTREAM PPLQATQDDV QVEIDVEQLE DRAGAGIVET 550 560 570 580 590 600 PRGAIKVTAQ PSDRVVGEYL VLTPQAVLRS QKLSLIHALA EQVKTCTHSG RAGRYAVEAY 610 620 630 640 650 660 DGRVLVPSGY AIPQEDFQSL SESATMVFNE REFVNRKLHH IAMHGPALNT DEESYELVRV 670 680 690 700 710 720 EKTEHEYVYD VDQKKCCKRE EATGLVLVGD LTSPPYHEFA YEGLKIRPAC PYKTAVIGVF 730 740 750 760 770 780 GVPGSGKSAI IKNLVTRQDL VTSGKKENCQ EISNDVMRQR KLEISARTVD SLLLNGCNKP 790 800 810 820 830 840 VEVLYVDEAF ACHSGTLLAL IAMVRPRQKV VLCGDPKQCG FFNMMQMKVN YNHNICTQVY 850 860 870 880 890 900 HKSISRRCTL PVTAIVSSLH YESKMRTTNE YNQPIVVDTT GITKPEPGDL VLTCFRGWVK 910 920 930 940 950 960 QLQIDYRGNE VMTAAASQGL TRKGVYAVRQ KVNENPLYAS TSEHVNVLLT RTEGKLIWKT 970 980 990 1000 1010 1020 LSGDPWIKIL QNPPKGNFKA TIKEWEAEHA SIMAGICNHQ MAFDTFQNKA NVCWAKCLVP 1030 1040 1050 1060 1070 1080 ILDTAGIKLS DRQWSQIVQA FKEDRAYSPE VALNEICTRI YGVDLDSGLF SKPLISVYYA 1090 1100 1110 1120 1130 1140 DNHWDNRPGG KMFGFNPEVA LMLEKKYPFT KGKWNINKQI CITTRKVDEF NPETNIIPAN 1150 1160 1170 1180 1190 1200 RRLPHSLVAE HHTVRGERME WLVNKINGHH MLLVSGYNLI LPTKRVTWVA PLGTRGADYT 1210 1220 1230 1240 1250 1260 YNLELGLPAT LGRYDLVVIN IHTPFRIHHY QQCVDHAMKL QMLGGDSLRL LKPGGSLLIR 1270 1280 1290 1300 1310 1320 AYGYADRTSE RVISVLGRKF RSSRALKPQC ITSNTEMFFL FSRFDNGRRN FTTHVMNNQL 1330 1340 1350 1360 1370 1380 NAVYAGLATR AGCAPSYRVK RMDIAKNTEE CVVNAANPRG VPGDGVCKAV YRKWPESFRN 1390 1400 1410 1420 1430 1440 SATPVGTAKT IMCGQYPVIH AVGPNFSNYS EAEGDRELAS VYREVAKEVS RLGVSSVAIP 1450 1460 1470 1480 1490 1500 LLSTGVYSGG KDRLLQSLNH LFTAMDSTDA DVVIYCRDKE WEKKITEAIS LRSQVELLDD 1510 1520 1530 1540 1550 1560 HISVDCDIVR VHPDSSLAGR KGYSTVEGAL YSYLEGTRFH QTAVDMAEIY TMWPKQTEAN 1570 1580 1590 1600 1610 1620 EQVCLYALGE SIESVRQKCP VDDADASFPP KTVPCLCRYA MTPERVARLR MNHTTSIIVC 1630 1640 1650 1660 1670 1680 SSFPLPKYKI EGVQKVKCSK ALLFDHNVPS RVSPRTYRPA DEIIQTPQIP TEACQDAQFV 1690 1700 1710 1720 1730 1740 QSITDEAVPV PSDLEACDAT MDWPSIDIVP TRQRSDSFDS EYSSRSNIQL VTADVHAPMY 1750 1760 1770 1780 1790 1800 ANSLASSGGS VLSLSSEQAQ NGIMILPDSE DTDSISRVST PIAPPRRRLG RTINVTCDER 1810 1820 1830 1840 1850 1860 EGKILPMASD RLFTAKPYTV ALGVSTADIT AYPIQAPLGS TQPPALEQIT FGDFAEGEID 1870 1880 1890 1900 1910 1920 NLLTGALTFG DFEPGEVEEL TDSEWSTCSD TDEELXLDRA GGYIFSSDTG QGHLQQKSVR 1930 1940 1950 1960 1970 1980 QTTLPVNIVE EVHEEKCYPP KLDEIKEQLL LKRLQESAST ANRSRYQSRK VENMKATIIH 1990 2000 2010 2020 2030 2040 RLKEGCRLYL ASDTPRVPSY RITYPAPVYS PSISIKLNNP ETAVAVCNEF LARNYPTVAS 2050 2060 2070 2080 2090 2100 YQVTDEYDAY LDMVDGSESC LDRATFNPSK LRSYPKQHSY HAPTIRSAVP SPFQNTLQNV 2110 2120 2130 2140 2150 2160 LAAATKRNCN VTQMRELPTM DSAVFNVECF KKYACNQEYW REFASSPIRV TTENLTMYVT 2170 2180 2190 2200 2210 2220 KLKGPKAAAL FAKTHNLLPL QEVPMDRFTM DMKRDVKVTP GTKHTEERPK VQVIQAAEPL 2230 2240 2250 2260 2270 2280 ATAYLCGIHR ELVRRLNAVL LPNVHTLFDM SAEDFDAIIS THFKPGDAVL ETDIASFDKS 2290 2300 2310 2320 2330 2340 QDDSLALTAM MLLEDLGVDQ PILDLIEAAF GEISSCHLPT GTRFKFGAMM KSGMFLTLFV 2350 2360 2370 2380 2390 2400 NTLLNITIAS RVLEERLTTS ACAAFIGDDN IIHGVVSDAL MAARCATWMN MEVKIIDAVV 2410 2420 2430 2440 2450 2460 SEKAPYFCGG FILHDTVTGT SCRVADPLKR LFKLGKPLAA GDEQDEDRRR ALADEVTRWQ 2470 2480 2490 2500 2510 RTGLITELEK AVYSRYEVQG ITAVITSMAT FASSKENFKK LRGPVVTLYG GPK

References

[1]

"Emergence of epidemic O'nyong-nyong fever in Uganda after a 35-year absence: genetic characterization of the virus." Lanciotti R.S., Ludwig M.L., Rwaguma E.B., Lutwama J.J., Kram T.M., Karabatsos N., Cropp B.C., Miller B.R. Virology 252:258-268(1998) [PubMed: 9875334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF079456 Genomic RNA. Translation: AAC97204.1.
3D structure databases
HSSP	HSSP built from PDB template 1FW5 based on UniProtKB P08411.
ModBase	Search...
Protein family/group databases
MEROPS	C09.001.
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. [Graphical view]
Pfam	PF01661. A1pp. 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_ONNVS

Accession

Primary (citable) accession number: O90368

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 4, 2006
Last sequence update:	November 1, 1998
Last modified:	November 25, 2008
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)