Reviewed, UniProtKB/Swiss-Prot P08411 (POLN_SFV)

Names and origin

Protein names	Recommended name:     Non-structural polyprotein Alternative name(s):     Polyprotein nsP1234       Short name(s)=P1234 Cleaved into 5 chains:   Recommended name:       P123   Recommended name:       mRNA-capping enzyme nsP1       EC=2.1.1.-       EC=2.7.7.-   Alternative name(s):       Non-structural protein 1   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(s)=nsP2   Recommended name:       Non-structural protein 3         Short name(s)=nsP3   Recommended name:       RNA-directed RNA polymerase nsP4       EC=2.7.7.48   Alternative name(s):       Non-structural protein 4         Short name(s)=nsP4
Organism	Semliki forest virus (SFV)
Taxonomic identifier	11033 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Togaviridae › Alphavirus › SFV complex
Virus host	Aedes [TaxID: 7158] Culex tritaeniorhynchus [TaxID: 7178] Atelerix albiventris (Middle-African hedgehog) [TaxID: 9368] Homo sapiens (Human) [TaxID: 9606] Rhipicephalus [TaxID: 34630] Quelea [TaxID: 158617] Halcyon [TaxID: 170865]

Protein attributes

Sequence length	2432 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein 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. 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. 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. nsP3 is essential for minus strand and subgenomic 26S mRNA synthesis. 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.
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.
Subcellular location	Non-structural polyprotein: Endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. 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 side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. mRNA-capping enzyme nsP1: Endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Cell projection › filopodium. 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. Protease/triphosphatase/NTPase/helicase nsP2: Endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Nucleus. 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. Non-structural protein 3: Endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasm. 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. RNA-directed RNA polymerase nsP4: Endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side.
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. 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.
Biophysicochemical properties	Kinetic parameters: KM=2.99 mM for triphosphatase (at pH 8.0) KM=90 mM for NTPase (at pH 7.5)

Ontologies

Keywords
Biological process	RNA replication mRNA capping mRNA processing
Cellular component	Cell membrane Cell projection 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	3D-structure Multifunctional enzyme
Gene Ontology (GO)
Cellular component	lysosomal membrane Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	nucleoside-triphosphatase activity Inferred from electronic annotation. Source: EC polynucleotide 5'-phosphatase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Molecule processing

Chain

1 – 2432

2432

Non-structural polyprotein

Chain

1 – 1818

1818

P123

Chain

1 – 537

537

mRNA-capping enzyme nsP1

Chain

538 – 1336

799

Protease/triphosphatase/NTPase/helicase nsP2

Chain

1337 – 1818

482

Non-structural protein 3

Chain

1819 – 2431

613

RNA-directed RNA polymerase nsP4

Regions

Domain

966 – 1167

202

Peptidase C9

Domain

1337 – 1495

159

Macro

Domain

2182 – 2297

116

RdRp catalytic

Nucleotide binding

723 – 730

8

ATP Potential

Region

245 – 264

20

nsP1 membrane-binding

Region

1007 – 1026

20

Nucleolus localization signal

Motif

1184 – 1188

5

Nuclear localization signal

Sites

Active site

1015

1

For cysteine protease nsP2 activity By similarity

Active site

1085

1

For cysteine protease nsP2 activity By similarity

Site

537 – 538

2

Cleavage; by nsP2

Site

1336 – 1337

2

Cleavage; by nsP2

Site

1818 – 1819

2

Cleavage; by nsP2

Amino acid modifications

Modified residue

1680

1

Phosphothreonine; by host

Modified residue

1681

1

Phosphothreonine; by host

Lipidation

418

1

S-palmitoyl cysteine; by host

Lipidation

420

1

S-palmitoyl cysteine; by host

Natural variations

Natural variant

6

1

H → Y in strain: Isolate L10.

Natural variant

95 – 96

2

VC → DS in strain: Isolate Garoff/Takkinen.

Natural variant

119

1

D → N in strain: Isolate Ts14.

Natural variant

311

1

E → K in strain: Isolate L10.

Natural variant

529

1

E → D in strain: Isolate Ts10.

Natural variant

596

1

R → G in strain: Isolate Garoff/Takkinen.

Natural variant

764 – 771

8

LDIQAKTV → KGTSRENS in strain: Isolate Garoff/Takkinen.

Natural variant

764 – 771

8

LDIQAKTV → NWTSRKNS in strain: Isolate L10.

Natural variant

817

1

D → N in strain: Isolate L10.

Natural variant

826

1

M → T in strain: Isolate L10.

Natural variant

843

1

H → N in strain: Isolate L10.

Natural variant

845

1

S → N in strain: Isolate Ts1.

Natural variant

859

1

S → C in strain: Isolate L10.

Natural variant

869

1

T → S in strain: Isolate Ts13.

Natural variant

901

1

V → A in strain: Isolate Garoff/Takkinen.

Natural variant

1114

1

G → R in strain: Isolate Ts11.

Natural variant

1199

1

A → T in strain: Isolate Ts6.

Natural variant

1258 – 1259

2

SL → I in strain: Isolate Garoff/Takkinen and Isolate L10.

Natural variant

1384

1

A → E in strain: Isolate L10 clone SFV4.

Natural variant

1565

1

Q → R in strain: Isolate Garoff/Takkinen.

Natural variant

1579

1

R → G in strain: Isolate Garoff/Takkinen.

Natural variant

1644

1

G → V in strain: Isolate Garoff/Takkinen, Isolate L10 and Isolate L10 clone SFV4.

Natural variant

1849

1

E → Q in strain: Isolate Garoff/Takkinen.

Natural variant

1921

1

P → R in strain: Isolate L10.

Natural variant

1938

1

V → A in strain: Isolate L10.

Natural variant

2060

1

A → V in strain: Isolate Ts13.

Natural variant

2088

1

A → D in strain: Isolate L10.

Natural variant

2405

1

A → T in strain: Isolate Garoff/Takkinen.

Experimental info

Mutagenesis

19

1

L → E: Complete loss of guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

38

1

H → A: Complete loss of guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

64

1

D → A: 60% increase of guanine-7-methyl transferase activity in vitro. Complete loss of guanylyltransferase activity in vitro

Mutagenesis

81 – 83

3

CVC → AVA: 60% loss of guanine-7-methyl transferase activity and complete loss of guanylyltransferase activity in vitro

Mutagenesis

90

1

D → A: Complete loss of guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

93

1

R → A: Complete loss of guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

135

1

C → A: 90% loss of guanine-7-methyl transferase activity and complete loss of guanylyltransferase activity in vitro

Mutagenesis

142

1

C → A: Complete loss of guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

153

1

D → A: No effect on guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

169

1

K → A: 50% loss of guanine-7-methyl transferase activity and no effect on guanylyltransferase activity in vitro

Mutagenesis

180

1

D → A: No effect on guanine-7-methyl transferase activity in vitro

Mutagenesis

203

1

E → A: No effect on guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

214

1

C → A: 90% loss of guanylyltransferase and guanine-7-methyl transferase activity in vitro

Mutagenesis

249

1

Y → A: 97% loss of guanine-7-methyl transferase activity and complete loss of guanylyltransferase activity in vitro

Mutagenesis

317

1

K → A: 95% loss of guanine-7-methyl transferase activity and 98% loss of guanylyltransferase activity in vitro

Mutagenesis

418 – 420

3

CCC → AAA: Complete loss of palmitoylation. Complete loss of pathogenicity in mice

Mutagenesis

729

1

K → N: Complete loss of NTPase and helicase activity

Mutagenesis

1015

1

C → A: Complete loss of polyprotein processing

Mutagenesis

1186

1

R → D: Complete loss of nuclear localization for nsP2

Mutagenesis

1680

1

T → A: Complete loss of threonine phosphorylation

Mutagenesis

1681

1

T → A: Complete loss of threonine phosphorylation

Mutagenesis

1824

1

D → A: No effect on polyprotein processing

Secondary structure

1

.

.

.

2432

Helix Strand Turn

Details...

Helix

246 – 259

14

Sequences

	Sequence		Length	Mass (Da)
	P08411-1 [UniParc]. Last modified March 21, 2006. Version 2. Checksum: BE7104A1EC3EF6EE	FASTA	2,432	269,512
	10 20 30 40 50 60 MAAKVHVDIE ADSPFIKSLQ KAFPSFEVES LQVTPNDHAN ARAFSHLATK LIEQETDKDT 70 80 90 100 110 120 LILDIGSAPS RRMMSTHKYH CVCPMRSAED PERLVCYAKK LAAASGKVLD REIAGKITDL 130 140 150 160 170 180 QTVMATPDAE SPTFCLHTDV TCRTAAEVAV YQDVYAVHAP TSLYHQAMKG VRTAYWIGFD 190 200 210 220 230 240 TTPFMFDALA GAYPTYATNW ADEQVLQARN IGLCAASLTE GRLGKLSILR KKQLKPCDTV 250 260 270 280 290 300 MFSVGSTLYT ESRKLLRSWH LPSVFHLKGK QSFTCRCDTI VSCEGYVVKK ITMCPGLYGK 310 320 330 340 350 360 TVGYAVTYHA EGFLVCKTTD TVKGERVSFP VCTYVPSTIC DQMTGILATD VTPEDAQKLL 370 380 390 400 410 420 VGLNQRIVVN GRTQRNTNTM KNYLLPIVAV AFSKWAREYK ADLDDEKPLG VRERSLTCCC 430 440 450 460 470 480 LWAFKTRKMH TMYKKPDTQT IVKVPSEFNS FVIPSLWSTG LAIPVRSRIK MLLAKKTKRE 490 500 510 520 530 540 LIPVLDASSA RDAEQEEKER LEAELTREAL PPLVPIAPAE TGVVDVDVEE LEYHAGAGVV 550 560 570 580 590 600 ETPRSALKVT AQPNDVLLGN YVVLSPQTVL KSSKLAPVHP LAEQVKIITH NGRAGRYQVD 610 620 630 640 650 660 GYDGRVLLPC GSAIPVPEFQ ALSESATMVY NEREFVNRKL YHIAVHGPSL NTDEENYEKV 670 680 690 700 710 720 RAERTDAEYV FDVDKKCCVK REEASGLVLV GELTNPPFHE FAYEGLKIRP SAPYKTTVVG 730 740 750 760 770 780 VFGVPGSGKS AIIKSLVTKH DLVTSGKKEN CQEIVNDVKK HRGLDIQAKT VDSILLNGCR 790 800 810 820 830 840 RAVDILYVDE AFACHSGTLL ALIALVKPRS KVVLCGDPKQ CGFFNMMQLK VNFNHNICTE 850 860 870 880 890 900 VCHKSISRRC TRPVTAIVST LHYGGKMRTT NPCNKPIIID TTGQTKPKPG DIVLTCFRGW 910 920 930 940 950 960 VKQLQLDYRG HEVMTAAASQ GLTRKGVYAV RQKVNENPLY APASEHVNVL LTRTEDRLVW 970 980 990 1000 1010 1020 KTLAGDPWIK VLSNIPQGNF TATLEEWQEE HDKIMKVIEG PAAPVDAFQN KANVCWAKSL 1030 1040 1050 1060 1070 1080 VPVLDTAGIR LTAEEWSTII TAFKEDRAYS PVVALNEICT KYYGVDLDSG LFSAPKVSLY 1090 1100 1110 1120 1130 1140 YENNHWDNRP GGRMYGFNAA TAARLEARHT FLKGQWHTGK QAVIAERKIQ PLSVLDNVIP 1150 1160 1170 1180 1190 1200 INRRLPHALV AEYKTVKGSR VEWLVNKVRG YHVLLVSEYN LALPRRRVTW LSPLNVTGAD 1210 1220 1230 1240 1250 1260 RCYDLSLGLP ADAGRFDLVF VNIHTEFRIH HYQQCVDHAM KLQMLGGDAL RLLKPGGSLL 1270 1280 1290 1300 1310 1320 MRAYGYADKI SEAVVSSLSR KFSSARVLRP DCVTSNTEVF LLFSNFDNGK RPSTLHQMNT 1330 1340 1350 1360 1370 1380 KLSAVYAGEA MHTAGCAPSY RVKRADIATC TEAAVVNAAN ARGTVGDGVC RAVAKKWPSA 1390 1400 1410 1420 1430 1440 FKGAATPVGT IKTVMCGSYP VIHAVAPNFS ATTEAEGDRE LAAVYRAVAA EVNRLSLSSV 1450 1460 1470 1480 1490 1500 AIPLLSTGVF SGGRDRLQQS LNHLFTAMDA TDADVTIYCR DKSWEKKIQE AIDMRTAVEL 1510 1520 1530 1540 1550 1560 LNDDVELTTD LVRVHPDSSL VGRKGYSTTD GSLYSYFEGT KFNQAAIDMA EILTLWPRLQ 1570 1580 1590 1600 1610 1620 EANEQICLYA LGETMDNIRS KCPVNDSDSS TPPRTVPCLC RYAMTAERIA RLRSHQVKSM 1630 1640 1650 1660 1670 1680 VVCSSFPLPK YHVDGVQKVK CEKGLLFDPT VPSVVSPRKY AASTTDHSDR SLRGFDLDWT 1690 1700 1710 1720 1730 1740 TDSSSTASDT MSLPSLQSCD IDSIYEPMAP IVVTADVHPE PAGIADLAAD VHPEPADHVD 1750 1760 1770 1780 1790 1800 LENPIPPPRP KRAAYLASRA AERPVPAPRK PTPAPRTAFR NKLPLTFGDF DEHEVDALAS 1810 1820 1830 1840 1850 1860 GITFGDFDDV LRLGRAGAYI FSSDTGSGHL QQKSVRQHNL QCAQLDAVEE EKMYPPKLDT 1870 1880 1890 1900 1910 1920 EREKLLLLKM QMHPSEANKS RYQSRKVENM KATVVDRLTS GARLYTGADV GRIPTYAVRY 1930 1940 1950 1960 1970 1980 PRPVYSPTVI ERFSSPDVAI AACNEYLSRN YPTVASYQIT DEYDAYLDMV DGSDSCLDRA 1990 2000 2010 2020 2030 2040 TFCPAKLRCY PKHHAYHQPT VRSAVPSPFQ NTLQNVLAAA TKRNCNVTQM RELPTMDSAV 2050 2060 2070 2080 2090 2100 FNVECFKRYA CSGEYWEEYA KQPIRITTEN ITTYVTKLKG PKAAALFAKT HNLVPLQEVP 2110 2120 2130 2140 2150 2160 MDRFTVDMKR DVKVTPGTKH TEERPKVQVI QAAEPLATAY LCGIHRELVR RLNAVLRPNV 2170 2180 2190 2200 2210 2220 HTLFDMSAED FDAIIASHFH PGDPVLETDI ASFDKSQDDS LALTGLMILE DLGVDQYLLD 2230 2240 2250 2260 2270 2280 LIEAAFGEIS SCHLPTGTRF KFGAMMKSGM FLTLFINTVL NITIASRVLE QRLTDSACAA 2290 2300 2310 2320 2330 2340 FIGDDNIVHG VISDKLMAER CASWVNMEVK IIDAVMGEKP PYFCGGFIVF DSVTQTACRV 2350 2360 2370 2380 2390 2400 SDPLKRLFKL GKPLTAEDKQ DEDRRRALSD EVSKWFRTGL GAELEVALTS RYEVEGCKSI 2410 2420 2430 LIAMATLARD IKAFKKLRGP VIHLYGGPRL VR

References

[1]	"Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus." Takkinen K. Nucleic Acids Res. 14:5667-5682(1986) [PubMed: 3488539] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Garoff/Takkinen.
[2]	"Replicase complex genes of Semliki Forest virus confer lethal neurovirulence." Tuittila M.T., Santagati M.G., Roeyttae M., Maeaettae J.A., Hinkkanen A.E. J. Virol. 74:4579-4589(2000) [PubMed: 10775594] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate L10 clone SFV4.
[3]	"Semliki Forest virus -- L10 strain complete genome." Logue C., Mooney D., Shanley R., Atkins G.J. Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate L10.
[4]	"Identification of mutations causing temperature-sensitive defects in Semliki Forest virus RNA synthesis." Lulla V., Merits A., Sarin P., Kaariainen L., Keranen S.,