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Non-structural polyprotein (Polyprotein nsP1234) (P1234) [Cleaved into: P123; mRNA-capping enzyme nsP1 (EC 2.1.1.-) (EC 2.7.7.-) (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) (Non-structural protein 2) (nsP2); Non-structural protein 3 (nsP3); RNA-directed RNA polymerase nsP4 (EC 2.7.7.48) (Non-structural protein 4) (nsP4)]

 POLN_SFV                Reviewed;        2432 AA.
P08411; Q3LRQ3; Q3LRQ4; Q3LRQ6; Q3LRQ7; Q3LRQ9; Q3LRR0; Q3LRR1;
Q3LRR2; Q8JMP6; Q9QBM1;
01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
21-MAR-2006, sequence version 2.
25-OCT-2017, entry version 150.
RecName: Full=Non-structural polyprotein;
AltName: Full=Polyprotein nsP1234;
Short=P1234;
Contains:
RecName: Full=P123;
Contains:
RecName: Full=mRNA-capping enzyme nsP1;
EC=2.1.1.-;
EC=2.7.7.-;
AltName: Full=Non-structural protein 1;
Contains:
RecName: Full=Protease nsP2;
EC=3.1.3.33;
EC=3.4.22.-;
EC=3.6.1.15;
EC=3.6.4.13;
AltName: Full=Non-structural protein 2;
Short=nsP2;
Contains:
RecName: Full=Non-structural protein 3;
Short=nsP3;
Contains:
RecName: Full=RNA-directed RNA polymerase nsP4;
EC=2.7.7.48;
AltName: Full=Non-structural protein 4;
Short=nsP4;
Semliki forest virus (SFV).
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage;
Togaviridae; Alphavirus; SFV complex.
NCBI_TaxID=11033;
NCBI_TaxID=7158; Aedes.
NCBI_TaxID=9368; Atelerix albiventris (Middle-African hedgehog) (Four-toed hedgehog).
NCBI_TaxID=7178; Culex tritaeniorhynchus (Mosquito).
NCBI_TaxID=170865; Halcyon.
NCBI_TaxID=9606; Homo sapiens (Human).
NCBI_TaxID=158617; Quelea.
NCBI_TaxID=34630; Rhipicephalus.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
STRAIN=Isolate Garoff/Takkinen;
PubMed=3488539; DOI=10.1093/nar/14.14.5667;
Takkinen K.;
"Complete nucleotide sequence of the nonstructural protein genes of
Semliki Forest virus.";
Nucleic Acids Res. 14:5667-5682(1986).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
STRAIN=Isolate L10 clone SFV4;
PubMed=10775594; DOI=10.1128/JVI.74.10.4579-4589.2000;
Tuittila M.T., Santagati M.G., Roeyttae M., Maeaettae J.A.,
Hinkkanen A.E.;
"Replicase complex genes of Semliki Forest virus confer lethal
neurovirulence.";
J. Virol. 74:4579-4589(2000).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
STRAIN=Isolate L10;
Logue C., Mooney D., Shanley R., Atkins G.J.;
"Semliki Forest virus -- L10 strain complete genome.";
Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
STRAIN=Isolate Ts1, Isolate Ts10, Isolate TS11, Isolate Ts13,
Isolate Ts14, Isolate Ts6, and Isolate Ts9;
PubMed=16501123; DOI=10.1128/JVI.80.6.3108-3111.2006;
Lulla V., Merits A., Sarin P., Kaariainen L., Keranen S., Ahola T.;
"Identification of mutations causing temperature-sensitive defects in
Semliki Forest virus RNA synthesis.";
J. Virol. 80:3108-3111(2006).
[5]
SUBCELLULAR LOCATION OF NON-STRUCTURAL PROTEINS.
PubMed=2904446; DOI=10.1083/jcb.107.6.2075;
Froshauer S., Kartenbeck J., Helenius A.;
"Alphavirus RNA replicase is located on the cytoplasmic surface of
endosomes and lysosomes.";
J. Cell Biol. 107:2075-2086(1988).
[6]
SUBCELLULAR LOCATION OF NSP2.
PubMed=1386484; DOI=10.1016/0042-6822(92)90570-F;
Rikkonen M., Peraenen J., Kaeaeriaeinen L.;
"Nuclear and nucleolar targeting signals of Semliki Forest virus
nonstructural protein nsP2.";
Virology 189:462-473(1992).
[7]
FUNCTION OF NSP2.
PubMed=8057461;
Rikkonen M., Peraenen J., Kaeaeriaeinen L.;
"ATPase and GTPase activities associated with Semliki Forest virus
nonstructural protein nsP2.";
J. Virol. 68:5804-5810(1994).
[8]
SUBCELLULAR LOCATION OF NSP1.
PubMed=7747433; DOI=10.1006/viro.1995.1192;
Peraenen J., Laakkonen P., Hyvoenen M., Kaeaeriaeinen L.;
"The alphavirus replicase protein nsP1 is membrane-associated and has
affinity to endocytic organelles.";
Virology 208:610-620(1995).
[9]
CHARACTERIZATION OF MRNA GUANYLYLTRANSFERASE FUNCTION OF NSP1.
PubMed=7831320; DOI=10.1073/pnas.92.2.507;
Ahola T., Kaeaeriaeinen L.;
"Reaction in alphavirus mRNA capping: formation of a covalent complex
of nonstructural protein nsP1 with 7-methyl-GMP.";
Proc. Natl. Acad. Sci. U.S.A. 92:507-511(1995).
[10]
PALMITOYLATION AT CYS-418 AND CYS-420, AND MUTAGENESIS OF
418-CYS--CYS-420.
PubMed=8910486; DOI=10.1074/jbc.271.45.28567;
Laakkonen P., Ahola T., Kaeaeriaeinen L.;
"The effects of palmitoylation on membrane association of Semliki
forest virus RNA capping enzyme.";
J. Biol. Chem. 271:28567-28571(1996).
[11]
SUBCELLULAR LOCATION OF NPS2, AND MUTAGENESIS OF ARG-1186.
PubMed=8610462; DOI=10.1006/viro.1996.0204;
Rikkonen M.;
"Functional significance of the nuclear-targeting and NTP-binding
motifs of Semliki Forest virus nonstructural protein nsP2.";
Virology 218:352-361(1996).
[12]
FUNCTION OF NSP1, AND MUTAGENESIS OF LEU-19; HIS-38; ASP-64;
81-CYS--CYS-83; ASP-90; ARG-93; CYS-135; CYS-142; ASP-153; LYS-169;
ASP-180; GLU-203; CYS-214; TYR-249 AND LYS-317.
PubMed=8985362;
Ahola T., Laakkonen P., Vihinen H., Kaeaeriaeinen L.;
"Critical residues of Semliki Forest virus RNA capping enzyme involved
in methyltransferase and guanylyltransferase-like activities.";
J. Virol. 71:392-397(1997).
[13]
FUNCTION OF NSP1.
PubMed=9811773;
Laakkonen P., Auvinen P., Kujala P., Kaeaeriaeinen L.;
"Alphavirus replicase protein NSP1 induces filopodia and rearrangement
of actin filaments.";
J. Virol. 72:10265-10269(1998).
[14]
MEMBRANE-BINDING OF NSP1.
PubMed=10357827; DOI=10.1093/emboj/18.11.3164;
Ahola T., Lampio A., Auvinen P., Kaeaeriaeinen L.;
"Semliki Forest virus mRNA capping enzyme requires association with
anionic membrane phospholipids for activity.";
EMBO J. 18:3164-3172(1999).
[15]
FUNCTION OF NSP2, AND MUTAGENESIS OF LYS-729.
PubMed=10217401; DOI=10.1016/S0014-5793(99)00321-X;
Gomez de Cedron M., Ehsani N., Mikkola M.L., Garcia J.A.,
Kaeaeriaeinen L.;
"RNA helicase activity of Semliki Forest virus replicase protein
NSP2.";
FEBS Lett. 448:19-22(1999).
[16]
PALMITOYLATION AT CYS-418 AND CYS-420, AND MUTAGENESIS OF
418-CYS--CYS-420.
PubMed=10888610; DOI=10.1128/JVI.74.15.6725-6733.2000;
Ahola T., Kujala P., Tuittila M., Blom T., Laakkonen P., Hinkkanen A.,
Auvinen P.;
"Effects of palmitoylation of replicase protein nsP1 on alphavirus
infection.";
J. Virol. 74:6725-6733(2000).
[17]
FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES OF NSP2.
PubMed=10748213; DOI=10.1074/jbc.M910340199;
Vasiljeva L., Merits A., Auvinen P., Kaeaeriaeinen L.;
"Identification of a novel function of the alphavirus capping
apparatus. RNA 5'-triphosphatase activity of Nsp2.";
J. Biol. Chem. 275:17281-17287(2000).
[18]
ACTIVE SITE OF NSP2 PROTEASE, AND MUTAGENESIS OF CYS-1015 AND
ASP-1824.
PubMed=11257180;
Merits A., Vasiljeva L., Ahola T., Kaeaeriaeinen L., Auvinen P.;
"Proteolytic processing of Semliki Forest virus-specific non-
structural polyprotein by nsP2 protease.";
J. Gen. Virol. 82:765-773(2001).
[19]
PHOSPHORYLATION AT THR-1680 AND THR-1681, AND MUTAGENESIS OF THR-1680
AND THR-1681.
PubMed=11104756; DOI=10.1074/jbc.M006077200;
Vihinen H., Ahola T., Tuittila M., Merits A., Kaeaeriaeinen L.;
"Elimination of phosphorylation sites of Semliki Forest virus
replicase protein nsP3.";
J. Biol. Chem. 276:5745-5752(2001).
[20]
PROTEOLYTIC PROCESSING OF POLYPROTEIN.
PubMed=12917405; DOI=10.1074/jbc.M307481200;
Vasiljeva L., Merits A., Golubtsov A., Sizemskaja V.,
Kaeaeriaeinen L., Ahola T.;
"Regulation of the sequential processing of Semliki Forest virus
replicase polyprotein.";
J. Biol. Chem. 278:41636-41645(2003).
[21]
INDUCTION.
PubMed=15930128; DOI=10.1091/mbc.E05-02-0124;
McInerney G.M., Kedersha N.L., Kaufman R.J., Anderson P.,
Liljestrom P.;
"Importance of eIF2alpha phosphorylation and stress granule assembly
in alphavirus translation regulation.";
Mol. Biol. Cell 16:3753-3763(2005).
[22]
INDUCTION.
PubMed=16391235; DOI=10.1101/gad.357006;
Ventoso I., Sanz M.A., Molina S., Berlanga J.J., Carrasco L.,
Esteban M.;
"Translational resistance of late alphavirus mRNA to eIF2alpha
phosphorylation: a strategy to overcome the antiviral effect of
protein kinase PKR.";
Genes Dev. 20:87-100(2006).
[23]
FUNCTION OF NSP2.
PubMed=16352561; DOI=10.1128/JVI.80.1.360-371.2006;
Sawicki D.L., Perri S., Polo J.M., Sawicki S.G.;
"Role for nsP2 proteins in the cessation of alphavirus minus-strand
synthesis by host cells.";
J. Virol. 80:360-371(2006).
[24]
FUNCTION OF NSP2.
PubMed=22514352; DOI=10.1128/JVI.00541-12;
Akhrymuk I., Kulemzin S.V., Frolova E.I.;
"Evasion of the innate immune response: the Old World alphavirus nsP2
protein induces rapid degradation of Rpb1, a catalytic subunit of RNA
polymerase II.";
J. Virol. 86:7180-7191(2012).
[25]
STRUCTURE BY NMR OF 245-264.
PubMed=10984480; DOI=10.1074/jbc.M004865200;
Lampio A., Kilpelainen I., Pesonen S., Karhi K., Auvinen P.,
Somerharju P., Kaeaeriaeinen L.;
"Membrane binding mechanism of an RNA virus-capping enzyme.";
J. Biol. Chem. 275:37853-37859(2000).
-!- 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.
-!- FUNCTION: 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.
-!- FUNCTION: 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. Also inhibits cellular
transcription by inducing rapid degradation of POLR2A, a catalytic
subunit of the RNAPII complex. The resulting inhibition of
cellular protein synthesis serves to ensure maximal viral gene
expression and to evade host immune response.
-!- FUNCTION: nsP3 is essential for minus strand and subgenomic 26S
mRNA synthesis.
-!- FUNCTION: nsP4 is an 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 codes for
structural proteins.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + GTP = m(7)GTP.
-!- CATALYTIC ACTIVITY: m7GTP + [nsP1 protein] = m7GMP-[nsP1 protein]
+ diphosphate.
-!- CATALYTIC ACTIVITY: m7GMP-[nsP1 protein] + (5')pp-Pur-mRNA =
m(7)G(5')ppp-Pur-mRNA + [nsP1 protein].
-!- CATALYTIC ACTIVITY: (5')ppp-mRNA + H(2)O = (5')pp-mRNA +
phosphate.
-!- CATALYTIC ACTIVITY: A 5'-phosphopolynucleotide + H(2)O = a
polynucleotide + phosphate.
-!- CATALYTIC ACTIVITY: NTP + H(2)O = NDP + phosphate.
-!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
-!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
+ RNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00539}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=2.99 mM for triphosphatase (at pH 8.0)
{ECO:0000269|PubMed:10748213};
KM=90 mM for NTPase (at pH 7.5) {ECO:0000269|PubMed:10748213};
-!- SUBUNIT: P123 interacts with nsP4; nsP1, nsP2, nsP3 and nsP4
interact with each other, and with uncharacterized host factors.
-!- SUBCELLULAR LOCATION: Non-structural polyprotein: Host endosome
membrane; Peripheral membrane protein; Cytoplasmic side. Host
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.
-!- SUBCELLULAR LOCATION: P123: Host endosome membrane; Peripheral
membrane protein; Cytoplasmic side. Host lysosome membrane;
Peripheral membrane protein; Cytoplasmic side.
-!- SUBCELLULAR LOCATION: mRNA-capping enzyme nsP1: Host endosome
membrane; Peripheral membrane protein; Cytoplasmic side. Host
lysosome membrane; Peripheral membrane protein; Cytoplasmic side.
Host cell membrane; Peripheral membrane protein; Cytoplasmic side.
Host cell projection, host 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.
-!- SUBCELLULAR LOCATION: Protease nsP2: Host endosome membrane
{ECO:0000269|PubMed:1386484}; Peripheral membrane protein
{ECO:0000269|PubMed:1386484}; Cytoplasmic side
{ECO:0000269|PubMed:1386484}. Host lysosome membrane
{ECO:0000269|PubMed:1386484}; Peripheral membrane protein
{ECO:0000269|PubMed:1386484}; Cytoplasmic side
{ECO:0000269|PubMed:1386484}. Host nucleus
{ECO:0000269|PubMed:1386484}. 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.
-!- SUBCELLULAR LOCATION: Non-structural protein 3: Host endosome
membrane; Peripheral membrane protein; Cytoplasmic side. Host
lysosome membrane; Peripheral membrane protein; Cytoplasmic side.
Host 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.
-!- SUBCELLULAR LOCATION: RNA-directed RNA polymerase nsP4: Host
endosome membrane; Peripheral membrane protein; Cytoplasmic side.
Host 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. {ECO:0000269|PubMed:15930128, ECO:0000269|PubMed:16391235}.
-!- PTM: 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. {ECO:0000269|PubMed:12917405}.
-!- PTM: nsP1 is palmitoylated by host. {ECO:0000269|PubMed:10888610,
ECO:0000269|PubMed:8910486}.
-!- PTM: nsP3 is phosphorylated by host on serines and threonines.
{ECO:0000269|PubMed:11104756}.
-!- PTM: nsP4 is ubiquitinated; targets the protein for rapid
degradation via the ubiquitin system. {ECO:0000250}.
-!- CAUTION: There is no stop codon readthrough before nsp4.
{ECO:0000305}.
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EMBL; X04129; CAA27741.1; -; Genomic_RNA.
EMBL; AJ251359; CAB62256.1; -; Genomic_RNA.
EMBL; AY112987; AAM64226.1; -; Genomic_RNA.
EMBL; DQ189079; ABA29023.1; -; Genomic_RNA.
EMBL; DQ189080; ABA29024.1; -; Genomic_RNA.
EMBL; DQ189081; ABA29025.1; -; Genomic_RNA.
EMBL; DQ189082; ABA29026.1; -; Genomic_RNA.
EMBL; DQ189083; ABA29028.1; -; Genomic_RNA.
EMBL; DQ189084; ABA29029.1; -; Genomic_RNA.
EMBL; DQ189085; ABA29031.1; -; Genomic_RNA.
EMBL; DQ189086; ABA29032.1; -; Genomic_RNA.
PIR; A23592; MNWVSF.
RefSeq; NP_463457.1; NC_003215.1.
PDB; 1FW5; NMR; -; A=245-264.
PDB; 5DRV; X-ray; 2.75 A; B=1785-1792.
PDB; 5FW5; X-ray; 1.92 A; C=1785-1809.
PDBsum; 1FW5; -.
PDBsum; 5DRV; -.
PDBsum; 5FW5; -.
ProteinModelPortal; P08411; -.
SMR; P08411; -.
ELM; P08411; -.
MEROPS; C09.001; -.
iPTMnet; P08411; -.
SwissPalm; P08411; -.
PRIDE; P08411; -.
GeneID; 922350; -.
KEGG; vg:922350; -.
OrthoDB; VOG09000007; -.
SABIO-RK; P08411; -.
EvolutionaryTrace; P08411; -.
Proteomes; UP000000570; Genome.
Proteomes; UP000100607; Genome.
Proteomes; UP000136172; Genome.
Proteomes; UP000166518; Genome.
Proteomes; UP000174511; Genome.
GO; GO:0044175; C:host cell endosome membrane; IEA:UniProtKB-SubCell.
GO; GO:0044176; C:host cell filopodium; IEA:UniProtKB-SubCell.
GO; GO:0044188; C:host cell lysosomal membrane; IEA:UniProtKB-SubCell.
GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
GO; GO:0020002; C:host cell plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0008234; F:cysteine-type peptidase activity; IEA:UniProtKB-KW.
GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
GO; GO:0008174; F:mRNA methyltransferase activity; IEA:InterPro.
GO; GO:0004651; F:polynucleotide 5'-phosphatase activity; IEA:UniProtKB-EC.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0006370; P:7-methylguanosine mRNA capping; IEA:UniProtKB-KW.
GO; GO:0039523; P:suppression by virus of host RNA polymerase II activity; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
InterPro; IPR027351; (+)RNA_virus_helicase_core_dom.
InterPro; IPR002588; Alphavirus-like_MT_dom.
InterPro; IPR002620; Alphavirus_nsp2pro.
InterPro; IPR002589; Macro_dom.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR007094; RNA-dir_pol_PSvirus.
InterPro; IPR001788; Tymovirus_RNA-dep_RNA_pol.
Pfam; PF01661; Macro; 1.
Pfam; PF01707; Peptidase_C9; 1.
Pfam; PF00978; RdRP_2; 1.
Pfam; PF01443; Viral_helicase1; 1.
Pfam; PF01660; Vmethyltransf; 1.
SMART; SM00506; A1pp; 1.
SUPFAM; SSF52540; SSF52540; 1.
PROSITE; PS51743; ALPHAVIRUS_MT; 1.
PROSITE; PS51154; MACRO; 1.
PROSITE; PS51520; NSP2PRO; 1.
PROSITE; PS51657; PSRV_HELICASE; 1.
PROSITE; PS50507; RDRP_SSRNA_POS; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome;
Eukaryotic host gene expression shutoff by virus;
Eukaryotic host transcription shutoff by virus; GTP-binding; Helicase;
Host cell membrane; Host cell projection; Host cytoplasm;
Host endosome; Host gene expression shutoff by virus; Host lysosome;
Host membrane; Host nucleus; Host-virus interaction; Hydrolase;
Inhibition of host RNA polymerase II by virus; Lipoprotein; Membrane;
Methyltransferase; mRNA capping; mRNA processing;
Multifunctional enzyme; Nucleotide-binding; Nucleotidyltransferase;
Palmitate; Phosphoprotein; Protease; Reference proteome;
RNA suppression of termination; RNA-binding;
RNA-directed RNA polymerase; S-adenosyl-L-methionine; Thiol protease;
Transferase; Ubl conjugation; Viral RNA replication.
CHAIN 1 2432 Non-structural polyprotein.
/FTId=PRO_0000308403.
CHAIN 1 1818 P123.
/FTId=PRO_0000227770.
CHAIN 1 537 mRNA-capping enzyme nsP1.
/FTId=PRO_0000041228.
CHAIN 538 1336 Protease nsP2.
/FTId=PRO_0000041229.
CHAIN 1337 1818 Non-structural protein 3.
/FTId=PRO_0000041230.
CHAIN 1819 2431 RNA-directed RNA polymerase nsP4.
/FTId=PRO_0000041231.
DOMAIN 29 260 Alphavirus-like MT. {ECO:0000255|PROSITE-
ProRule:PRU01079}.
DOMAIN 692 844 (+)RNA virus helicase ATP-binding.
DOMAIN 845 993 (+)RNA virus helicase C-terminal.
DOMAIN 1006 1329 Peptidase C9. {ECO:0000255|PROSITE-
ProRule:PRU00853}.
DOMAIN 1337 1495 Macro. {ECO:0000255|PROSITE-
ProRule:PRU00490}.
DOMAIN 2182 2297 RdRp catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00539}.
NP_BIND 723 730 ATP. {ECO:0000255}.
REGION 245 264 nsP1 membrane-binding.
REGION 1007 1026 Nucleolus localization signal.
MOTIF 1184 1188 Nuclear localization signal.
ACT_SITE 1015 1015 For cysteine protease nsP2 activity.
{ECO:0000255|PROSITE-ProRule:PRU00853}.
ACT_SITE 1085 1085 For cysteine protease nsP2 activity.
{ECO:0000255|PROSITE-ProRule:PRU00853}.
SITE 537 538 Cleavage; by nsP2.
SITE 1336 1337 Cleavage; by nsP2.
SITE 1818 1819 Cleavage; by nsP2.
MOD_RES 1680 1680 Phosphothreonine; by host.
{ECO:0000269|PubMed:11104756}.
MOD_RES 1681 1681 Phosphothreonine; by host.
{ECO:0000269|PubMed:11104756}.
LIPID 418 418 S-palmitoyl cysteine; by host.
{ECO:0000269|PubMed:10888610,
ECO:0000269|PubMed:8910486}.
LIPID 420 420 S-palmitoyl cysteine; by host.
{ECO:0000269|PubMed:10888610,
ECO:0000269|PubMed:8910486}.
VARIANT 6 6 H -> Y (in strain: Isolate L10).
VARIANT 95 96 VC -> DS (in strain: Isolate Garoff/
Takkinen).
VARIANT 119 119 D -> N (in strain: Isolate Ts14).
VARIANT 311 311 E -> K (in strain: Isolate L10).
VARIANT 529 529 E -> D (in strain: Isolate Ts10).
VARIANT 596 596 R -> G (in strain: Isolate Garoff/
Takkinen).
VARIANT 764 771 LDIQAKTV -> KGTSRENS (in strain: Isolate
Garoff/Takkinen).
VARIANT 764 771 LDIQAKTV -> NWTSRKNS (in strain: Isolate
L10).
VARIANT 817 817 D -> N (in strain: Isolate L10).
VARIANT 826 826 M -> T (in strain: Isolate L10).
VARIANT 843 843 H -> N (in strain: Isolate L10).
VARIANT 845 845 S -> N (in strain: Isolate Ts1).
VARIANT 859 859 S -> C (in strain: Isolate L10).
VARIANT 869 869 T -> S (in strain: Isolate Ts13).
VARIANT 901 901 V -> A (in strain: Isolate Garoff/
Takkinen).
VARIANT 1114 1114 G -> R (in strain: Isolate Ts11).
VARIANT 1199 1199 A -> T (in strain: Isolate Ts6).
VARIANT 1258 1259 SL -> I (in strain: Isolate Garoff/
Takkinen and Isolate L10).
VARIANT 1384 1384 A -> E (in strain: Isolate L10 clone
SFV4).
VARIANT 1565 1565 Q -> R (in strain: Isolate Garoff/
Takkinen).
VARIANT 1579 1579 R -> G (in strain: Isolate Garoff/
Takkinen).
VARIANT 1644 1644 G -> V (in strain: Isolate Garoff/
Takkinen, Isolate L10 and Isolate L10
clone SFV4).
VARIANT 1849 1849 E -> Q (in strain: Isolate Garoff/
Takkinen).
VARIANT 1921 1921 P -> R (in strain: Isolate L10).
VARIANT 1938 1938 V -> A (in strain: Isolate L10).
VARIANT 2060 2060 A -> V (in strain: Isolate Ts13).
VARIANT 2088 2088 A -> D (in strain: Isolate L10).
VARIANT 2405 2405 A -> T (in strain: Isolate Garoff/
Takkinen).
MUTAGEN 19 19 L->E: Complete loss of
guanylyltransferase and guanine-7-methyl
transferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 38 38 H->A: Complete loss of
guanylyltransferase and guanine-7-methyl
transferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 64 64 D->A: 60% increase of guanine-7-methyl
transferase activity in vitro. Complete
loss of guanylyltransferase activity in
vitro. {ECO:0000269|PubMed:8985362}.
MUTAGEN 81 83 CVC->AVA: 60% loss of guanine-7-methyl
transferase activity and complete loss of
guanylyltransferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 90 90 D->A: Complete loss of
guanylyltransferase and guanine-7-methyl
transferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 93 93 R->A: Complete loss of
guanylyltransferase and guanine-7-methyl
transferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 135 135 C->A: 90% loss of guanine-7-methyl
transferase activity and complete loss of
guanylyltransferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 142 142 C->A: Complete loss of
guanylyltransferase and guanine-7-methyl
transferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 153 153 D->A: No effect on guanylyltransferase
and guanine-7-methyl transferase activity
in vitro. {ECO:0000269|PubMed:8985362}.
MUTAGEN 169 169 K->A: 50% loss of guanine-7-methyl
transferase activity and no effect on
guanylyltransferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 180 180 D->A: No effect on guanine-7-methyl
transferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 203 203 E->A: No effect on guanylyltransferase
and guanine-7-methyl transferase activity
in vitro. {ECO:0000269|PubMed:8985362}.
MUTAGEN 214 214 C->A: 90% loss of guanylyltransferase and
guanine-7-methyl transferase activity in
vitro. {ECO:0000269|PubMed:8985362}.
MUTAGEN 249 249 Y->A: 97% loss of guanine-7-methyl
transferase activity and complete loss of
guanylyltransferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 317 317 K->A: 95% loss of guanine-7-methyl
transferase activity and 98% loss of
guanylyltransferase activity in vitro.
{ECO:0000269|PubMed:8985362}.
MUTAGEN 418 420 CCC->AAA: Complete loss of
palmitoylation. Complete loss of
pathogenicity in mice.
{ECO:0000269|PubMed:10888610,
ECO:0000269|PubMed:8910486}.
MUTAGEN 729 729 K->N: Complete loss of NTPase and
helicase activity.
{ECO:0000269|PubMed:10217401}.
MUTAGEN 1015 1015 C->A: Complete loss of polyprotein
processing.
{ECO:0000269|PubMed:11257180}.
MUTAGEN 1186 1186 R->D: Complete loss of nuclear
localization for nsP2.
{ECO:0000269|PubMed:8610462}.
MUTAGEN 1680 1680 T->A: Complete loss of threonine
phosphorylation.
{ECO:0000269|PubMed:11104756}.
MUTAGEN 1681 1681 T->A: Complete loss of threonine
phosphorylation.
{ECO:0000269|PubMed:11104756}.
MUTAGEN 1824 1824 D->A: No effect on polyprotein
processing.
{ECO:0000269|PubMed:11257180}.
HELIX 246 259 {ECO:0000244|PDB:1FW5}.
STRAND 1786 1789 {ECO:0000244|PDB:5DRV}.
HELIX 1794 1799 {ECO:0000244|PDB:5FW5}.
SEQUENCE 2432 AA; 269512 MW; BE7104A1EC3EF6EE CRC64;
MAAKVHVDIE ADSPFIKSLQ KAFPSFEVES LQVTPNDHAN ARAFSHLATK LIEQETDKDT
LILDIGSAPS RRMMSTHKYH CVCPMRSAED PERLVCYAKK LAAASGKVLD REIAGKITDL
QTVMATPDAE SPTFCLHTDV TCRTAAEVAV YQDVYAVHAP TSLYHQAMKG VRTAYWIGFD
TTPFMFDALA GAYPTYATNW ADEQVLQARN IGLCAASLTE GRLGKLSILR KKQLKPCDTV
MFSVGSTLYT ESRKLLRSWH LPSVFHLKGK QSFTCRCDTI VSCEGYVVKK ITMCPGLYGK
TVGYAVTYHA EGFLVCKTTD TVKGERVSFP VCTYVPSTIC DQMTGILATD VTPEDAQKLL
VGLNQRIVVN GRTQRNTNTM KNYLLPIVAV AFSKWAREYK ADLDDEKPLG VRERSLTCCC
LWAFKTRKMH TMYKKPDTQT IVKVPSEFNS FVIPSLWSTG LAIPVRSRIK MLLAKKTKRE
LIPVLDASSA RDAEQEEKER LEAELTREAL PPLVPIAPAE TGVVDVDVEE LEYHAGAGVV
ETPRSALKVT AQPNDVLLGN YVVLSPQTVL KSSKLAPVHP LAEQVKIITH NGRAGRYQVD
GYDGRVLLPC GSAIPVPEFQ ALSESATMVY NEREFVNRKL YHIAVHGPSL NTDEENYEKV
RAERTDAEYV FDVDKKCCVK REEASGLVLV GELTNPPFHE FAYEGLKIRP SAPYKTTVVG
VFGVPGSGKS AIIKSLVTKH DLVTSGKKEN CQEIVNDVKK HRGLDIQAKT VDSILLNGCR
RAVDILYVDE AFACHSGTLL ALIALVKPRS KVVLCGDPKQ CGFFNMMQLK VNFNHNICTE
VCHKSISRRC TRPVTAIVST LHYGGKMRTT NPCNKPIIID TTGQTKPKPG DIVLTCFRGW
VKQLQLDYRG HEVMTAAASQ GLTRKGVYAV RQKVNENPLY APASEHVNVL LTRTEDRLVW
KTLAGDPWIK VLSNIPQGNF TATLEEWQEE HDKIMKVIEG PAAPVDAFQN KANVCWAKSL
VPVLDTAGIR LTAEEWSTII TAFKEDRAYS PVVALNEICT KYYGVDLDSG LFSAPKVSLY
YENNHWDNRP GGRMYGFNAA TAARLEARHT FLKGQWHTGK QAVIAERKIQ PLSVLDNVIP
INRRLPHALV AEYKTVKGSR VEWLVNKVRG YHVLLVSEYN LALPRRRVTW LSPLNVTGAD
RCYDLSLGLP ADAGRFDLVF VNIHTEFRIH HYQQCVDHAM KLQMLGGDAL RLLKPGGSLL
MRAYGYADKI SEAVVSSLSR KFSSARVLRP DCVTSNTEVF LLFSNFDNGK RPSTLHQMNT
KLSAVYAGEA MHTAGCAPSY RVKRADIATC TEAAVVNAAN ARGTVGDGVC RAVAKKWPSA
FKGAATPVGT IKTVMCGSYP VIHAVAPNFS ATTEAEGDRE LAAVYRAVAA EVNRLSLSSV
AIPLLSTGVF SGGRDRLQQS LNHLFTAMDA TDADVTIYCR DKSWEKKIQE AIDMRTAVEL
LNDDVELTTD LVRVHPDSSL VGRKGYSTTD GSLYSYFEGT KFNQAAIDMA EILTLWPRLQ
EANEQICLYA LGETMDNIRS KCPVNDSDSS TPPRTVPCLC RYAMTAERIA RLRSHQVKSM
VVCSSFPLPK YHVDGVQKVK CEKGLLFDPT VPSVVSPRKY AASTTDHSDR SLRGFDLDWT
TDSSSTASDT MSLPSLQSCD IDSIYEPMAP IVVTADVHPE PAGIADLAAD VHPEPADHVD
LENPIPPPRP KRAAYLASRA AERPVPAPRK PTPAPRTAFR NKLPLTFGDF DEHEVDALAS
GITFGDFDDV LRLGRAGAYI FSSDTGSGHL QQKSVRQHNL QCAQLDAVEE EKMYPPKLDT
EREKLLLLKM QMHPSEANKS RYQSRKVENM KATVVDRLTS GARLYTGADV GRIPTYAVRY
PRPVYSPTVI ERFSSPDVAI AACNEYLSRN YPTVASYQIT DEYDAYLDMV DGSDSCLDRA
TFCPAKLRCY PKHHAYHQPT VRSAVPSPFQ NTLQNVLAAA TKRNCNVTQM RELPTMDSAV
FNVECFKRYA CSGEYWEEYA KQPIRITTEN ITTYVTKLKG PKAAALFAKT HNLVPLQEVP
MDRFTVDMKR DVKVTPGTKH TEERPKVQVI QAAEPLATAY LCGIHRELVR RLNAVLRPNV
HTLFDMSAED FDAIIASHFH PGDPVLETDI ASFDKSQDDS LALTGLMILE DLGVDQYLLD
LIEAAFGEIS SCHLPTGTRF KFGAMMKSGM FLTLFINTVL NITIASRVLE QRLTDSACAA
FIGDDNIVHG VISDKLMAER CASWVNMEVK IIDAVMGEKP PYFCGGFIVF DSVTQTACRV
SDPLKRLFKL GKPLTAEDKQ DEDRRRALSD EVSKWFRTGL GAELEVALTS RYEVEGCKSI
LIAMATLARD IKAFKKLRGP VIHLYGGPRL VR


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