Reviewed, UniProtKB/Swiss-Prot Q8JUX6 (POLN_CHIKS)

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	Chikungunya virus (strain S27-African prototype) (CHIKV)
Taxonomic identifier	371094 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus › SFV complex
Virus host	Aedes aegypti (Yellowfever mosquito) [TaxID: 7159] Aedes albopictus (Forest day mosquito) [TaxID: 7160] Cercopithecus [TaxID: 9533] Macaca (macaques) [TaxID: 9539] Papio (baboons) [TaxID: 9554] Presbytis [TaxID: 9573] Pan troglodytes (Chimpanzee) [TaxID: 9598] Homo sapiens (Human) [TaxID: 9606] Aedes polynesiensis [TaxID: 188700] Aedes furcifer [TaxID: 299627]

Protein attributes

Sequence length	2474 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 and its filopodial extensions 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 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 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)
Cellular component	lysosomal membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view
Molecule processing
	Chain	1 – 2474	2474	Non-structural polyprotein
	Chain	1 – 1863	1863	P123 By similarity
	Chain	1 – 535	535	mRNA-capping enzyme nsP1 By similarity
	Chain	536 – 1333	798	Protease/triphosphatase/NTPase/helicase nsP2 By similarity
	Chain	1334 – 1863	530	Non-structural protein 3 By similarity
	Chain	1864 – 2474	611	RNA-directed RNA polymerase nsP4 By similarity
Regions
	Domain	964 – 1165	202	Peptidase C9
	Domain	1334 – 1493	160	Macro
	Domain	2228 – 2343	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	1863 – 1864	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)
	Q8JUX6-1 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: 97D250B9EB5A3BB0	FASTA	2,474	275,652
	10 20 30 40 50 60 MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDHANA RAFSHLAIKL IEQEIDPDST 70 80 90 100 110 120 ILDIGSAPAR RMMSDRKYHC VCPMRSAEDP ERLANYARKL ASAAGKVLDR NISGKIGDLQ 130 140 150 160 170 180 AVMAVPDTET PTFCLHTDVS CRQRADVAIY QDVYAVHAPT SLYHQAIKGV RLAYWVGFDT 190 200 210 220 230 240 TPFMYNAMAG AYPSYSTNWA DEQVLKAKNI GLCSTDLTEG RRGKLSIMRG KKLEPCDRVL 250 260 270 280 290 300 FSVGSTLYPE SRKLLKSWHL PSVFHLKGKL SFTCRCDTVV SCEGYVVKRI TMSPGLYGKT 310 320 330 340 350 360 TGYAVTHHAD GFLMCKTTDT VDGERVSFSV CTYVPATICD QMTGILATEV TPEDAQKLLV 370 380 390 400 410 420 GLNQRIVVNG RTQRNTNTMK NYMIPVVAQA FSKWAKECRK DMEDEKLLGV RERTLTCCCL 430 440 450 460 470 480 WAFKKQKTHT VYKRPDTQSI QKVQAEFDSF VVPSLWSSGL SIPLRTRIKW LLSKVPKTDL 490 500 510 520 530 540 TPYSGDAQEA RDAEKEAEEE REAELTLEAL PPLQAAQEDV QVEIDVEQLE DRAGAGIIET 550 560 570 580 590 600 PRGAIKVTAQ PTDHVVGEYL VLSPQTVLRS QKLSLIHALA EQVKTCTHSG RAGRYAVEAY 610 620 630 640 650 660 DGRVLVPSGY AISPEDFQSL SESATMVYNE REFVNRKLHH IAMHGPALNT DEESYELVRA 670 680 690 700 710 720 ERTEHEYVYD VDQRRCCKKE EAAGLVLVGD LTNPPYHEFA YEGLKIRPAC PYKIAVIGVF 730 740 750 760 770 780 GVPGSGKSAI IKNLVTRQDL VTSGKKENCQ EITTDVMRQR GLEISARTVD SLLLNGCNRP 790 800 810 820 830 840 VDVLYVDEAF ACHSGTLLAL IALVRPRQKV VLCGDPKQCG FFNMMQMKVN YNHNICTQVY 850 860 870 880 890 900 HKSISRRCTL PVTAIVSSLH YEGKMRTTNE YNKPIVVDTT GSTKPDPGDL VLTCFRGWVK 910 920 930 940 950 960 QLQIDYRGHE VMTAAASQGL TRKGVYAVRQ KVNENPLYAS TSEHVNVLLT RTEGKLVWKT 970 980 990 1000 1010 1020 LSGDPWIKTL QNPPKGNFKA TIKEWEVEHA SIMAGICSHQ MTFDTFQNKA NVCWAKSLVP 1030 1040 1050 1060 1070 1080 ILETAGIKLN DRQWSQIIQA FKEDKAYSPE VALNEICTRM YGVDLDSGLF SKPLVSVYYA 1090 1100 1110 1120 1130 1140 DNHWDNRPGG KMFGFNPEAA SILERKYPFT KGKWNINKQI CVTTRRIEDF NPTTNIIPAN 1150 1160 1170 1180 1190 1200 RRLPHSLVAE HRPVKGERME WLVNKINGHH VLLVSGCSLA LPTKRVTWVA PLGVRGADYT 1210 1220 1230 1240 1250 1260 YNLELGLPAT LGRYDLVVIN IHTPFRIHHY QQCVDHAMKL QMLGGDSLRL LKPGGSLLIR 1270 1280 1290 1300 1310 1320 AYGYADRTSE RVICVLGRKF RSSRALKPPC VTSNTEMFFL FSNFDNGRRN FTTHVMNNQL 1330 1340 1350 1360 1370 1380 NAAFVGQATR AGCAPSYRVK RMDIAKNDEE CVVNAANPRG LPGDGVCKAV YKKWPESFKN 1390 1400 1410 1420 1430 1440 SATPVGTAKT VMCGTYPVIH AVGPNFSNYS ESEGDRELAA AYREVAKEVT RLGVNSVAIP 1450 1460 1470 1480 1490 1500 LLSTGVYSGG KDRLTQSLNH LFTAMDSTDA DVVIYCRDKE WEKKISEAIQ MRTQVELLDE 1510 1520 1530 1540 1550 1560 HISIDCDVVR VHPDSSLAGR KGYSTTEGAL YSYLEGTRFH QTAVDMAEIY TMWPKQTEAN 1570 1580 1590 1600 1610 1620 EQVCLYALGE SIESIRQKCP VDDADASSPP KTVPCLCRYA MTPERVTRLR MNHVTSIIVC 1630 1640 1650 1660 1670 1680 SSFPLPKYKI EGVQKVKCSK VMLFDHNVPS RVSPREYRPS QESVQEASTT TSLTHSQFDL 1690 1700 1710 1720 1730 1740 SVDGKILPVP SDLDADAPAL EPALDDGAIH TLPSATGNLA AVSDWVMSTV PVAPPRRRRG 1750 1760 1770 1780 1790 1800 RNLTVTCDER EGNITPMASV RFFRAELCPV VQETAETRDT AMSLQAPPST ATELSHPPIS 1810 1820 1830 1840 1850 1860 FGAPSETFPI TFGDFNEGEI ESLSSELLTF GDFLPGEVDD LTDSDWSTCS DTDDELRLDR 1870 1880 1890 1900 1910 1920 AGGYIFSSDT GPGHLQQKSV RQSVLPVNTL EEVHEEKCYP PKLDEAKEQL LLKKLQESAS 1930 1940 1950 1960 1970 1980 MANRSRYQSR KVENMKATII QRLKRGCRLY LMSETPKVPT YRTTYPAPVY SPPINVRLSN 1990 2000 2010 2020 2030 2040 PESAVAACNE FLARNYPTVS SYQITDEYDA YLDMVDGSES CLDRATFNPS KLRSYPKQHA 2050 2060 2070 2080 2090 2100 YHAPSIRSAV PSPFQNTLQN VLAAATKRNC NVTQMRELPT LDSAVFNVEC FKKFACNQEY 2110 2120 2130 2140 2150 2160 WEEFAASPIR ITTENLTTYV TKLKGPKAAA LFAKTHNLLP LQEVPMDRFT VDMKRDVKVT 2170 2180 2190 2200 2210 2220 PGTKHTEERP KVQVIQAAEP LATAYLCGIH RELVRRLNAV LLPNVHTLFD MSAEDFDAII 2230 2240 2250 2260 2270 2280 AAHFKPGDTV LETDIASFDK SQDDSLALTA LMLLEDLGVD HSLLDLIEAA FGEISSCHLP 2290 2300 2310 2320 2330 2340 TGTRFKFGAM MKSGMFLTLF VNTLLNITIA SRVLEDRLTK SACAAFIGDD NIIHGVVSDE 2350 2360 2370 2380 2390 2400 LMAARCATWM NMEVKIIDAV VSQKAPYFCG GFILHDIVTG TACRVADPLK RLFKLGKPLA 2410 2420 2430 2440 2450 2460 AGDEQDEDRR RALADEVVRW QRTGLIDELE KAVYSRYEVQ GISVVVMSMA TFASSRSNFE 2470 KLRGPVVTLY GGPK

References

[1]	"Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site." Khan A.H., Morita K., Parquet Md Mdel C., Hasebe F., Mathenge E.G., Igarashi A. J. Gen. Virol. 83:3075-3084(2002) [PubMed: 12466484] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF369024 Genomic RNA. Translation: AAN05101.1.
RefSeq	NP_690588.1.
3D structure databases
HSSP	HSSP built from PDB template 1FW5 based on UniProtKB P08411.
ModBase	Search...
Protein family/group databases
MEROPS	C09.001.
Genome annotation databases
GeneID	956309.
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]
ProDom	Q8JUX6. [Graphical view] [Entries sharing at least one domain]
BLOCKS	Search...
Other Resources
ProtoNet	Search...

Entry information

Entry name

POLN_CHIKS

Accession

Primary (citable) accession number: Q8JUX6

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 21, 2006
Last sequence update:	October 1, 2002
Last modified:	September 2, 2008
This is version 42 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)