Q5XXP4 (POLN_CHIK3) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Non-structural polyprotein Alternative name(s): Polyprotein nsP1234 Short name=P1234 Cleaved into the following 5 chains: P123 mRNA-capping enzyme nsP1 EC=2.1.1.- EC=2.7.7.- Alternative name(s): Non-structural protein 1 Protease nsP2 EC=3.1.3.33 EC=3.4.22.- EC=3.6.1.15 EC=3.6.4.13 Alternative name(s): Non-structural protein 2 Short name=nsP2 Non-structural protein 3 Short name=nsP3 RNA-directed RNA polymerase nsP4 EC=2.7.7.48 Alternative name(s): Non-structural protein 4 Short name=nsP4
Organism	Chikungunya virus (strain 37997) (CHIKV) [Complete proteome]
Taxonomic identifier	371095 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus › SFV complex
Virus host	Aedes aegypti (Yellowfever mosquito) (Culex aegypti) [TaxID: 7159] Aedes albopictus (Asian tiger mosquito) (Culex albopictus) [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 (Polynesian tiger mosquito) [TaxID: 188700] Aedes furcifer (Mosquito) [TaxID: 299627]

Protein attributes

Sequence length	2474 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. ATP + H2O = ADP + 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: 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 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. 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
Coding sequence diversity	RNA suppression of termination
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 Phosphoprotein Ubl conjugation
Technical term	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological process	mRNA capping Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular component	host cell endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host cell lysosomal membrane 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 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-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW helicase activity Inferred from electronic annotation. Source: UniProtKB-KW 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 – 2474	2474	Non-structural polyprotein		PRO_0000308396
	Chain	1 – 1863	1863	P123 By similarity		PRO_0000227765
	Chain	1 – 535	535	mRNA-capping enzyme nsP1 By similarity		PRO_0000227766
	Chain	536 – 1333	798	Protease nsP2 By similarity		PRO_0000227767
	Chain	1334 – 1863	530	Non-structural protein 3 By similarity		PRO_0000227768
	Chain	1864 – 2474	611	RNA-directed RNA polymerase nsP4 By similarity		PRO_0000227769
Regions
	Domain	1004 – 1327	324	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)
	Q5XXP4 [UniParc]. Last modified November 23, 2004. Version 1. Checksum: 0699DB0485FB3097	FASTA	2,474	275,933
	10 20 30 40 50 60 MDPVYVDIDA DSAFLKALQR AYPMFEVEPR QVTPNDHANA RAFSHLAIKL IEQEIDPDST 70 80 90 100 110 120 ILDIGSAPAR RMMSDRKYHC VCPMRSAEDP ERLANYARKL ASAAGKVLDR NISEKIGDLQ 130 140 150 160 170 180 AVMAVPDAET PTFCLHTDVS CRQRADVAIY QDVYAVHAPT SLYHQAIKGV RVAYWIGFDT 190 200 210 220 230 240 TPFMYNAMAG AYPSYSTNWA DEQVLKAKNI GLCSTDLTEG RRGKLSIMRG KKMKPCDRVL 250 260 270 280 290 300 FSVGSTLYPE SRKLLKSWHL PSVFHLKGKL SFTCRCDTVV SCEGYVVKRI TISPGLYGKT 310 320 330 340 350 360 TGYAVTHHAD GFLMCKTTDT VDGERVSFSV CTYVPATICD QMTGILATEV TPEDAQKLLV 370 380 390 400 410 420 GLNQRIVVNG RTQRNTNTMK NYLLPVVAQA FSKWAKECRK DMEDEKLLGI RERTLTCCCL 430 440 450 460 470 480 WAFKKQKTHT VYKRPDTQSI QKVPAEFDSF VVPSLWSSGL SIPLRTRIKW LLSKVPKTDL 490 500 510 520 530 540 IPYSGDAKEA RDAEKEAEEE REAELTREAL PPLQAAQDDV QVEIDVEQLE DRAGAGIIET 550 560 570 580 590 600 PRGAIKVTAQ PTDHVVGEYL VLSPQTVLRS QKLSLIHALA EQVKTCTHSG RAGRYAVEAY 610 620 630 640 650 660 DGRILVPSGY AISPEDFQSL SESATMVYNE REFVNRKLHH IALHGPALNT DEESYELVRA 670 680 690 700 710 720 ERTEHEYVYD VDQRRCCKKE EAAGLVLVGD LTNPPYHEFA YEGLRIRPAC PYKTAVIGVF 730 740 750 760 770 780 GVPGSGKSAI IKNLVTRQDL VTSGKKENCQ EISTDVMRQR NLEISARTVD 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 SIMAGICNHQ VTFDTFQNKA NVCWAKSLVP 1030 1040 1050 1060 1070 1080 ILETAGIKLN DRQWSQIIQA FKEDRAYSPE VALNEICTRM YGVDLDSGLF SKPLVSVHYA 1090 1100 1110 1120 1130 1140 DNHWDNRPGG KMFGFNPEAA SILERKYPFT KGKWNTNKQI CVTTRRIEDF NPNTNIIPAN 1150 1160 1170 1180 1190 1200 RRLPHSLVAE HRPVKGERME WLVNKINGHH VLLVSGYNLV LPTKRVTWVA PLGIRGADYT 1210 1220 1230 1240 1250 1260 YNLELGLPAT LGRYDLVIIN IHTPFRIHHY QQCVDHAMKL QMLGGDSLRL LKPGGSLLIR 1270 1280 1290 1300 1310 1320 AYGYADRTSE RVVCVLGRKF 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 LFTALDSTDA DVVIYCRDKE WEKKIAEAIQ MRTQVELLDE 1510 1520 1530 1540 1550 1560 HISVDCDIIR VHPDSSLAGR KGYSTTEGSL YSYLEGTRFH QTAVDMAEVY TMWPKQTEAN 1570 1580 1590 1600 1610 1620 EQVCLYALGE SIESIRQKCP VDDADASSPP KTVPCLCRYA MTPERVTRLR MNHVTSIIVC 1630 1640 1650 1660 1670 1680 SSFPLPKYKI EGVQKVKCSK VMLFDHNVPS RVSPREYKSP QETAQEVSST TSLTHSQFDL 1690 1700 1710 1720 1730 1740 SVDGEELPAP SDLEADAPIP EPTPDDRAVL TLPPTIDNFS AVSDWVMNTA PVAPPRRRRG 1750 1760 1770 1780 1790 1800 KNLNVTCDER EGNVLPMASV RFFRADLHSI VQETAEIRDT AASLQAPLSV ATEPNQLPIS 1810 1820 1830 1840 1850 1860 FGAPNETFPI TFGDFDEGEI ESLSSELLTF GDFSPGEVDD LTDSDWSTCS DTDDELXLDR 1870 1880 1890 1900 1910 1920 AGGYIFSSDT GPGHLQQRSV RQTVLPVNTL EEVQEEKCYP PKLDEVKEQL LLKKLQESAS 1930 1940 1950 1960 1970 1980 MANRSRYQSR KVENMKATIV QRLKGGCKLY LMSETPKVPT YRTTYPAPVY SPPINIRLSN 1990 2000 2010 2020 2030 2040 PESAVAACNE FLARNYPTVA SYQITDEYDA YLDMVDGSES CLDRATFNPS KLRSYPKQHS 2050 2060 2070 2080 2090 2100 YHAPTIRSAV PSPFQNTLQN VLAAATKRNC NVTQMRELPT LDSAVFNVEC FKKFACNQEY 2110 2120 2130 2140 2150 2160 WKEFAASPIR ITTENLTTYV TKLKGPKAAA LFAKTHNLLP LQEVPMDRFT VDMKRDVKVT 2170 2180 2190 2200 2210 2220 PGTKHTEERP KVQVIQAAEP LATAYLCGIH RELVRRLNAV LLPNVHTLFD MSAEDFDAII 2230 2240 2250 2260 2270 2280 AAHFKPGDAV LETDIASFDK SQDDSLALTA LMLLEDLGVD HPLLDLIEAA FGEISSCHLP 2290 2300 2310 2320 2330 2340 TGTRFKFGAM MKSGMFLTLF VNTLLNITIA SRVLEDRLTR SACAAFIGDD NIIHGVVSDE 2350 2360 2370 2380 2390 2400 LMAARCATWM NMEVKIIDAV VSQKAPYFCG GFILYDTVAG TACRVADPLK RLFKLGKPLA 2410 2420 2430 2440 2450 2460 AGDEQDDDRR RALADEVVRW QRTGLTDELE KAVHSRYEVQ GISVVVMSMA TFASSRSNFE 2470 KLRGPVVTLY GGPK

References

[1]

"Differential infectivities of O'Nyong-Nyong and Chikungunya virus isolates in Anopheles gambiae and Aedes aegypti mosquitoes." Vanlandingham D.L., Hong C., Klingler K., Tsetsarkin K., McElroy K.L., Powers A.M., Lehane M.J., Higgs S. Am. J. Trop. Med. Hyg. 72:616-621(2005) [PubMed: 15891138] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY726732 Genomic RNA. Translation: AAU43880.1.
3D structure databases
ProteinModelPortal	Q5XXP4.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR002589. A1pp. IPR000606. Helicase_domain_viral-like. IPR002620. Pept_C9_alphavirus_nsp2pro. IPR007094. RNA-dir_pol_PSvirus. IPR001788. Tymovirus_RNA-dep_RNA_pol. [Graphical view]
Pfam	PF01661. Macro. 1 hit. PF01707. Peptidase_C9. 1 hit. PF00978. RdRP_2. 1 hit. PF01443. Viral_helicase1. 1 hit. [Graphical view]
SMART	SM00506. A1pp. 1 hit. [Graphical view]
PROSITE	PS51154. MACRO. 1 hit. PS51520. NSP2PRO. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLN_CHIK3

Accession

Primary (citable) accession number: Q5XXP4

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 21, 2006
Last sequence update:	November 23, 2004
Last modified:	November 16, 2011
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program