Reviewed, UniProtKB/Swiss-Prot P13887 (POLN_RRVN)

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	Ross river virus (strain NB5092) (RRV)
Taxonomic identifier	11031 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus › SFV complex
Virus host	Aedes [TaxID: 7158] Macropus sp. (kangaroo) [TaxID: 9322] Homo sapiens (Human) [TaxID: 9606] Culex annulirostris (Common banded mosquito) [TaxID: 162997]

Protein attributes

Sequence length	2479 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 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/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. nsP3 is phosphorylated by host on serines and threonines. 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 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 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 – 2479	2479	Non-structural polyprotein		PRO_0000308400
	Chain	1 – 1868	1868	P123		PRO_0000229031
	Chain	1 – 533	533	mRNA-capping enzyme nsP1		PRO_0000041218
	Chain	534 – 1331	798	Protease/triphosphatase/NTPase/helicase nsP2		PRO_0000041219
	Chain	1332 – 1868	537	Non-structural protein 3		PRO_0000041220
	Chain	1869 – 2479	611	RNA-directed RNA polymerase nsP4		PRO_0000041221
Regions
	Domain	962 – 1162	201	Peptidase C9
	Domain	1332 – 1491	160	Macro
	Domain	2233 – 2348	116	RdRp catalytic
	Nucleotide binding	719 – 726	8	ATP Potential
	Region	242 – 261	20	nsP1 membrane-binding By similarity
	Region	1003 – 1022	20	Nucleolus localization signal By similarity
	Motif	1179 – 1183	5	Nuclear localization signal By similarity
Sites
	Active site	1011	1	For cysteine protease nsP2 activity By similarity
	Active site	1080	1	For cysteine protease nsP2 activity By similarity
	Site	533 – 534	2	Cleavage; by nsP2 By similarity
	Site	1331 – 1332	2	Cleavage; by nsP2 By similarity
	Site	1868 – 1869	2	Cleavage; by nsP2 By similarity
Amino acid modifications
	Modified residue	1675	1	Phosphothreonine; by host By similarity
	Lipidation	415	1	S-palmitoyl cysteine; by host By similarity
	Lipidation	417	1	S-palmitoyl cysteine; by host By similarity

Sequences

	Sequence		Length	Mass (Da)
	P13887-1 [UniParc]. Last modified January 1, 1990. Version 1. Checksum: E306EBAFDFF02CAB	FASTA	2,479	276,446
	10 20 30 40 50 60 MKVTVDVEAD SPFLKALQKA FPAFEVESQQ VTPNDHANAR AFSHLATKLI EQEVPANITI 70 80 90 100 110 120 LDVGSAPARR LMSDHSYHCI CPMKSAEDPE RLANYARKLA KTAGEVLDKN VSGKITDLQD 130 140 150 160 170 180 VMATPDLESP TFCLHTDETC RTRAEVAVYQ DVXXHAPTSL YHQAMKGVRT VYWIGFDTTP 190 200 210 220 230 240 FMFEVVAGAY PTYSTNWADE QVLQARNIGL CATSLSEGHR GKISIMRKKR LRPSDRXMFS 250 260 270 280 290 300 VGXTLYIESR RLLKSWHLPS VFHLKGKNSF TCRCDTIVSC EGYVVKKITM SPGTYGKTVG 310 320 330 340 350 360 YAVTHHAEGF LMCKVTDTVR GERVSFPVCT YVPATICDQM TGILATDVTP EDAQKLLVGL 370 380 390 400 410 420 NQRIVVNGRT QRNTNTMKNY LLPVVAQAFS KWAREAKADM EDEKPLGTRE RTLTCCCLWA 430 440 450 460 470 480 FKNHKTHTMY KRPDTQTIVK VPSTFDSFVI PSLWSSSLSI GIRQRIKLLL GPKLSRDLPY 490 500 510 520 530 540 SGDRNEAREA EKEAEETKEA ELTREALPPL VGSNCADDVD QVDVEELTYR AGAGVVETPR 550 560 570 580 590 600 NALKVTPQER DQLIGAYLIL SPQTVLKSEK LTPIHPLAEQ VTIMTHSGRS GRYPVDRYDG 610 620 630 640 650 660 RVLVPTGAAI PVSEFQALSE SATMVYNERE FINRKLHHIA LYGPALNTDE ENYEKVRAER 670 680 690 700 710 720 AEAEYVFDVD KRTCVKREDA SGLVLVGDLI NPPFHEFAYE GLKIRPATPF QTTVIGVFGV 730 740 750 760 770 780 PGSGKSAIIK SVVTTRDLVA SGKKENCQEI VNDVKKQRGL DVTARTVDSI LLNGCRRGVE 790 800 810 820 830 840 NLYVDEAFAC HSGTLLALIA MVKPTGKVIL CGDPKQCGFF NLMQLKVNFN HDICTQVLHK 850 860 870 880 890 900 SISRRCTLPI TAIVSTLHYQ GKMRTTNLCS APIQIDTTGT TKPAKGDIVL TCFRXWVKQL 910 920 930 940 950 960 QIDYRGHEVM TAAASQGLTR KGVYAVRQKV NENPLYAPSS EHVNVLLTRT ENRLVWKTLS 970 980 990 1000 1010 1020 GDPWIKVLTN IPKGDFSATL EEWQEEHDNI MNALRERSTA VDPFQNKAKV CWAKCLVQVL 1030 1040 1050 1060 1070 1080 ETAGIRMTAE EWDTVLAFRE DRAYSPEVAL NEICTKYYGV DLDSGLFSAQ SVSLYYENNH 1090 1100 1110 1120 1130 1140 WDNRPGGRMY GFNREVARKF EQRYPFLRGK MDSGLQVNVP ERKVQPFNAE CNILLLNRRL 1150 1160 1170 1180 1190 1200 PHALVTSYQQ CRGERVEWLL KKLPGYHLLL VSEYNLALPH KRVFWIAPPH VSGADRIYDL 1210 1220 1230 1240 1250 1260 DLGLPLNAGR YDLVFVNIHT EYRTHHYQQC VDHSMKLQML GGDSLHLLXP GGSLLIRAYG 1270 1280 1290 1300 1310 1320 YADRVSEMVV TALARKFSAF RVLRPACVTS NTEVFLLFTN FDNGRRAVTL HQANQRLSSM 1330 1340 1350 1360 1370 1380 FACNGLHTAG CAPSYRVRRT DISGHAEEAV VNAANAKGTV GVGVCRAVAR KWPDSFKGAA 1390 1400 1410 1420 1430 1440 TPVGTAKLVQ ANGMNVIHAV GPNFSTVTEA EGDRELAAAY RAVAGIINAS NIKSVAIPLL 1450 1460 1470 1480 1490 1500 STGVFSGGKD RVMQSLNHLF TAMDTTDADV VIYCRDKAWE KKIQEAIDRR TAVELVSEDI 1510 1520 1530 1540 1550 1560 SLESDLIRVH PDSCLVGRKG YSITDGKLHS YLEGTRFHQT AVDMAEISTL WPKLQDANEQ 1570 1580 1590 1600 1610 1620 ICLYALGESM DSIRTKCPVE DADSSTPPKT VPCLCRYAMT AERVARLRMN NTKAIIVCSS 1630 1640 1650 1660 1670 1680 FPLPKYRIEG VQKVKCDRVL IFDQTVPSLV SPRKYIPAAA SMHADTVSLD STVSTGSAWS 1690 1700 1710 1720 1730 1740 FPSEATYETM EVVAEVHHSE PPVPPPRRRR AQVTMHHQEL LEVSDMHTPI AARVEIPVYD 1750 1760 1770 1780 1790 1800 TAVVAERVAI PCTSEYATPI PTPRAVRVVP VPAPRIQRAS TYRVSPTPTP RVLRASVCSV 1810 1820 1830 1840 1850 1860 TTSAGVEFPW APEDLEVLTE PVHCEMREPV ELPWEPEDVD IQFGDFETPD KIQFGDIDFD 1870 1880 1890 1900 1910 1920 QFLSRAGAYI FSSDTGPGHL QQKSVRQHAL PCEMLYAHEE ERTYPPALDE AREKLLQAKM 1930 1940 1950 1960 1970 1980 QMAPTEANKS RYQSRKVENM KAVIIDRLKD GARTYLAEQS EKIPTYASKY PRPVYSPSVE 1990 2000 2010 2020 2030 2040 DSLQSPEVAV AACNAFLEAN YPTVASYQIT DEYDAYLDMV DGSESCLDRA TFCPAKLRCY 2050 2060 2070 2080 2090 2100 PKHHAYHQPQ VRSAVPSPFQ NTLQNVLAAA TKRNCNVTQM RELPTLDSAV FNVECFKKFA 2110 2120 2130 2140 2150 2160 CNGEYWQEFK DDPIRITTEN ITTYVTRLKG PKAAALFAKT HNLVPLQEVP MDRFVVDMKR 2170 2180 2190 2200 2210 2220 DVKVTPGTKH TEERPKVQVI QAAEPLATAY LCGIHRELVR RLKAVLAPNI HTLFDMSAED 2230 2240 2250 2260 2270 2280 FDAIIAAHFQ PGDAVLETDI ASFDKSQDDS LALTALMLLE DLGVDQELLD LIEEAFGEIT 2290 2300 2310 2320 2330 2340 SVHLPTGTRF KFGAMMKSGM FLTLFINTLL NIVIACRVLR EKLTNSICAA FIGDDNIVHG 2350 2360 2370 2380 2390 2400 VRSDPLMAER CASWVNMEVK IIDATMCEKP PYFCGGFILY DNVTGSACRV ADPLKRLFKL 2410 2420 2430 2440 2450 2460 GKPLPAGDTQ DEDRRRALKD ETDRWARVGL KSELEIALSS RYEVNGTGNI VRAMATLAKS 2470 LKNFKKLRGP IVHLYGGPK

References

[1]	"Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus." Faragher S.G., Meek A.D.J., Rice C.M., Dalgarno L. Virology 163:509-526(1988) [PubMed: 2833022] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	M20162 Genomic RNA. Translation: AAA96329.1. Sequence problems.
PIR	MNWVRA. A28605.
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. 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_RRVN

Accession

Primary (citable) accession number: P13887

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 1, 1990
Last modified:	June 16, 2009
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)