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P35207 (SKI2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 138. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Antiviral helicase SKI2

EC=3.6.4.13
Alternative name(s):
Superkiller protein 2
Gene names
Name:SKI2
Ordered Locus Names:YLR398C
ORF Names:L8084.17
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length1287 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

RNA helicase component of the SKI complex involved in 3'-mRNA degradation pathway. Represses dsRNA virus propagation by specifically blocking translation of viral mRNAs, perhaps recognizing the absence of CAP or poly(A). Essential for cell growth only in the presence of M1 replicon. Ref.1 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.18

Catalytic activity

ATP + H2O = ADP + phosphate.

Subunit structure

Component of the SKI complex composed of at least SKI2, SKI3 and SKI8. The SKI complex interacts with SKI7, which makes the link between the SKI complex and the exosome in order to perform mRNA degradation. Ref.11

Subcellular location

Cytoplasm Ref.11 Ref.16.

Miscellaneous

Present with 5770 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the helicase family. SKI2 subfamily.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Ontologies

Keywords
   Biological processAntiviral defense
Translation regulation
   Cellular componentCytoplasm
   LigandATP-binding
DNA-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processdefense response to virus

Inferred from electronic annotation. Source: UniProtKB-KW

nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay

Inferred from mutant phenotype PubMed 12881429. Source: SGD

nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'

Inferred from mutant phenotype Ref.10Ref.9. Source: SGD

nuclear-transcribed mRNA catabolic process, non-stop decay

Inferred from mutant phenotype PubMed 11910110PubMed 17660569. Source: SGD

regulation of translation

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentSki complex

Inferred from direct assay Ref.11PubMed 18042677. Source: SGD

cytoplasm

Inferred from direct assay PubMed 23222640. Source: SGD

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent helicase activity

Inferred from electronic annotation. Source: InterPro

DNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA helicase activity

Inferred from sequence or structural similarity Ref.1. Source: SGD

protein binding

Inferred from physical interaction Ref.11PubMed 16043509PubMed 16429126PubMed 23953113. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

SKI3P1788310EBI-1851,EBI-1861
SKI8Q0279310EBI-1851,EBI-17260

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12871287Antiviral helicase SKI2
PRO_0000102084

Regions

Domain338 – 496159Helicase ATP-binding
Domain638 – 815178Helicase C-terminal
Nucleotide binding351 – 3588ATP Potential
Region556 – 57722RNA-binding RGG-box By similarity
Motif444 – 4474DEVH box
Compositional bias555 – 59743Arg/Gly-rich

Amino acid modifications

Modified residue2091Phosphoserine Ref.19 Ref.20 Ref.21

Experimental info

Sequence conflict3261W → C in AAA35049. Ref.1
Sequence conflict759 – 7602QM → L in AAA35049. Ref.1

Secondary structure

............................................................................................................................................ 1287
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P35207 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: 7CCD36CFC0DF8C32

FASTA1,287146,059
        10         20         30         40         50         60 
MSEGFSSSSI QELYQSLKEI TNNADVELFE DRITKLDFES TDEPKHANDI IKDRFLRPSN 

        70         80         90        100        110        120 
ALPWSLLDMV QDVPHTSSPE DCSGKLDYKE LLKVPDPINR TSYQFKRTGL EGKISGYKEE 

       130        140        150        160        170        180 
VDLKEVANAN ASNSLSITRS INHNQNSVRG STAQLPFTPG GIPMKSVKTD SEQNGSSTMA 

       190        200        210        220        230        240 
NATKLLHKDG QGLFDIPEGM NRGIKPMDSP AENEDQNGQF KELKQLNEID NELDIRIEAN 

       250        260        270        280        290        300 
EAKLKEEEKS AKSISEEIME EATEETTADN ADDAEIDELL PIGIDFGRTK PVSKSVPVKK 

       310        320        330        340        350        360 
EWAHVVDLNH KIENFDELIP NPARSWPFEL DTFQKEAVYH LEQGDSVFVA AHTSAGKTVV 

       370        380        390        400        410        420 
AEYAIAMAHR NMTKTIYTSP IKALSNQKFR DFKETFDDVN IGLITGDVQI NPDANCLIMT 

       430        440        450        460        470        480 
TEILRSMLYR GADLIRDVEF VIFDEVHYVN DQDRGVVWEE VIIMLPQHVK FILLSATVPN 

       490        500        510        520        530        540 
TYEFANWIGR TKQKNIYVIS TPKRPVPLEI NIWAKKELIP VINQNSEFLE ANFRKHKEIL 

       550        560        570        580        590        600 
NGESAKGAPS KTDNGRGGST ARGGRGGSNT RDGRGGRGNS TRGGANRGGS RGAGAIGSNK 

       610        620        630        640        650        660 
RKFFTQDGPS KKTWPEIVNY LRKRELLPMV VFVFSKKRCE EYADWLEGIN FCNNKEKSQI 

       670        680        690        700        710        720 
HMFIEKSITR LKKEDRDLPQ ILKTRSLLER GIAVHHGGLL PIVKELIEIL FSKGFIKVLF 

       730        740        750        760        770        780 
ATETFAMGLN LPTRTVIFSS IRKHDGNGLR ELTPGEFTQM AGRAGRRGLD STGTVIVMAY 

       790        800        810        820        830        840 
NSPLSIATFK EVTMGVPTRL QSQFRLTYNM ILNLLRIEAL RVEEMIKYSF SENAKETLQP 

       850        860        870        880        890        900 
EHEKQIKVLQ EELQTIEYKS CEICDNDIEK FLELMLAYKE ATVNLMQEMV KSPSILHILK 

       910        920        930        940        950        960 
EGRLVAFRDP NDCLKLGFVF KVSLKDAVCV IMTFTKPYKL PNGEPNHLIY FPKADGYRRR 

       970        980        990       1000       1010       1020 
NFPKFQKTDF YMEEVPVTAI EVITKRKFAA PLGKVIKKDV AALNEFNAET NNILDGKTLK 

      1030       1040       1050       1060       1070       1080 
EAINIEKQGL KIHQILLDRT NIRDEIFKLK SIKCPNLSQH IVPKFKAHVI KKKIEELYHL 

      1090       1100       1110       1120       1130       1140 
MSDQNLSLLP DYEKRLAVLK DTEFIDQNHN VLLKGRVACE INSGYELVLT ELILDNFLGS 

      1150       1160       1170       1180       1190       1200 
FEPEEIVALL SVFVYEGKTR EEEPPIVTPR LAKGKQRIEE IYKKMLCVFN THQIPLTQDE 

      1210       1220       1230       1240       1250       1260 
AEFLDRKRFA MMNVVYEWAR GLSFKEIMEM SPEAEGTVVR VITWLDEICR EVKTASIIIG 

      1270       1280 
NSTLHMKMSR AQELIKRDIV FAASLYL 

« Hide

References

« Hide 'large scale' references
[1]"Evidence that the SKI antiviral system of Saccharomyces cerevisiae acts by blocking expression of viral mRNA."
Widner W.R., Wickner R.B.
Mol. Cell. Biol. 13:4331-4341(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. expand/collapse author list , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"The yeast BDF1 gene encodes a transcription factor involved in the expression of a broad class of genes including snRNAs."
Lygerou Z., Conesa C., Lesage P., Swanson R.N., Ruet A., Carlson M., Sentenac A., Seraphin B.
Nucleic Acids Res. 22:5332-5340(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-162.
Strain: ATCC 204508 / S288c.
[5]"Chromosomal superkiller mutants of Saccharomyces cerevisiae."
Toh-e A., Guerry P., Wickner R.B.
J. Bacteriol. 136:1002-1007(1978) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[6]"Superkiller mutations in Saccharomyces cerevisiae suppress exclusion of M2 double-stranded RNA by L-A-HN and confer cold sensitivity in the presence of M and L-A-HN."
Ridley S.P., Sommer S.S., Wickner R.B.
Mol. Cell. Biol. 4:761-770(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[7]"Synthetic lethality of sep1 (xrn1) ski2 and sep1 (xrn1) ski3 mutants of Saccharomyces cerevisiae is independent of killer virus and suggests a general role for these genes in translation control."
Johnson A.W., Kolodner R.D.
Mol. Cell. Biol. 15:2719-2727(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Decoying the cap- mRNA degradation system by a double-stranded RNA virus and poly(A)- mRNA surveillance by a yeast antiviral system."
Masison D.C., Blanc A., Ribas J.C., Carroll K., Sonenberg N., Wickner R.B.
Mol. Cell. Biol. 15:2763-2771(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[9]"The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex."
Anderson J.S.J., Parker R.P.
EMBO J. 17:1497-1506(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[10]"Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs."
van Hoof A., Lennertz P., Parker R.
Mol. Cell. Biol. 20:441-452(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[11]"The yeast antiviral proteins Ski2p, Ski3p, and Ski8p exist as a complex in vivo."
Brown J.T., Bai X., Johnson A.W.
RNA 6:449-457(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH SKI3 AND SKI8, SUBCELLULAR LOCATION.
[12]"3' poly(A) is dispensable for translation."
Searfoss A.M., Wickner R.B.
Proc. Natl. Acad. Sci. U.S.A. 97:9133-9137(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[13]"Ski7p G protein interacts with the exosome and the Ski complex for 3'-to-5' mRNA decay in yeast."
Araki Y., Takahashi S., Kobayashi T., Kajiho H., Hoshino S., Katada T.
EMBO J. 20:4684-4693(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE SKI COMPLEX.
[14]"A cis-acting element known to block 3' mRNA degradation enhances expression of polyA-minus mRNA in wild-type yeast cells and phenocopies a ski mutant."
Brown J.T., Johnson A.W.
RNA 7:1566-1577(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE SKI COMPLEX.
[15]"An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation."
Mitchell P., Tollervey D.
Mol. Cell 11:1405-1413(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[16]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[17]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[18]"Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus."
Kushner D.B., Lindenbach B.D., Grdzelishvili V.Z., Noueiry A.O., Paul S.M., Ahlquist P.
Proc. Natl. Acad. Sci. U.S.A. 100:15764-15769(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[19]"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-209, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[20]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-209, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[21]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-209, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[22]"Structure-based assembly of protein complexes in yeast."
Aloy P., Boettcher B., Ceulemans H., Leutwein C., Mellwig C., Fischer S., Gavin A.-C., Bork P., Superti-Furga G., Serrano L., Russell R.B.
Science 303:2026-2029(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: MODELING OF THE SKI COMPLEX 3D-STRUCTURE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L13469 mRNA. Translation: AAA35049.1.
U19729 Genomic DNA. Translation: AAB82356.1.
Z18944 Genomic DNA. Translation: CAA79378.1.
BK006945 Genomic DNA. Translation: DAA09699.1.
PIRS55954.
RefSeqNP_013502.3. NM_001182286.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4A4KX-ray3.25A/C/E/G/I835-1085[»]
4A4ZX-ray2.40A296-1287[»]
4BUJX-ray3.70A/E1-834[»]
A/E1086-1287[»]
ProteinModelPortalP35207.
SMRP35207. Positions 299-549, 600-1287.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31657. 130 interactions.
DIPDIP-5887N.
IntActP35207. 14 interactions.
MINTMINT-662639.
STRING4932.YLR398C.

Proteomic databases

MaxQBP35207.
PaxDbP35207.
PeptideAtlasP35207.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYLR398C; YLR398C; YLR398C.
GeneID851114.
KEGGsce:YLR398C.

Organism-specific databases

CYGDYLR398c.
SGDS000004390. SKI2.

Phylogenomic databases

eggNOGCOG4581.
GeneTreeENSGT00750000117758.
HOGENOMHOG000163048.
KOK12599.
OMAVIIMLPD.
OrthoDBEOG7WT48P.

Enzyme and pathway databases

BioCycYEAST:G3O-32462-MONOMER.

Gene expression databases

GenevestigatorP35207.

Family and domain databases

Gene3D3.40.50.300. 3 hits.
InterProIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR012961. DSH_C.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR016438. RNA_helicase_ATP-dep_SK12/DOB1.
IPR025696. rRNA_proc-arch_dom.
[Graphical view]
PfamPF00270. DEAD. 1 hit.
PF08148. DSHCT. 1 hit.
PF00271. Helicase_C. 1 hit.
PF13234. rRNA_proc-arch. 1 hit.
[Graphical view]
PIRSFPIRSF005198. Antiviral_helicase_SKI2. 1 hit.
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 3 hits.
PROSITEPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio967830.
PROP35207.

Entry information

Entry nameSKI2_YEAST
AccessionPrimary (citable) accession number: P35207
Secondary accession number(s): D6VZ33, Q06047
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: May 30, 2000
Last modified: July 9, 2014
This is version 138 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XII

Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references