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P16658

- SEN2_YEAST

UniProt

P16658 - SEN2_YEAST

Protein

tRNA-splicing endonuclease subunit SEN2

Gene

SEN2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 137 (01 Oct 2014)
      Sequence version 1 (01 Aug 1990)
      Previous versions | rss
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    Functioni

    Constitutes one of the two catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3'-cyclic phosphate and 5'-OH termini. There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. This subunit may anchor the endonuclease complex to the nuclear membrane. Probably carries the active site for 5'-splice site cleavage.1 Publication

    Catalytic activityi

    PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei289 – 2891By similarity
    Active sitei297 – 2971By similarity
    Active sitei328 – 3281By similarity

    GO - Molecular functioni

    1. lyase activity Source: UniProtKB-KW
    2. nucleic acid binding Source: InterPro
    3. protein binding Source: IntAct
    4. tRNA-intron endonuclease activity Source: SGD

    GO - Biological processi

    1. RNA phosphodiester bond hydrolysis Source: GOC
    2. RNA phosphodiester bond hydrolysis, endonucleolytic Source: GOC
    3. tRNA-type intron splice site recognition and cleavage Source: SGD

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    tRNA processing

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16148.
    YEAST:G3O-32253-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA-splicing endonuclease subunit SEN2 (EC:4.6.1.16)
    Alternative name(s):
    Splicing endonuclease protein 2
    tRNA-intron endonuclease SEN2
    Gene namesi
    Name:SEN2
    Ordered Locus Names:YLR105C
    ORF Names:L8004.12
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XII

    Organism-specific databases

    CYGDiYLR105c.
    SGDiS000004095. SEN2.

    Subcellular locationi

    Nucleus 1 Publication. Endomembrane system 1 Publication; Peripheral membrane protein 1 Publication. Mitochondrion outer membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication
    Note: The tRNA splicing endonuclease complex is predominantly associated with the outer membrane of mitochondria, suggesting that tRNA splicing mainly takes place on the mitochondrial surface.

    GO - Cellular componenti

    1. endomembrane system Source: UniProtKB-SubCell
    2. mitochondrial outer membrane Source: SGD
    3. tRNA-intron endonuclease complex Source: SGD

    Keywords - Cellular componenti

    Membrane, Mitochondrion, Mitochondrion outer membrane, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 377377tRNA-splicing endonuclease subunit SEN2PRO_0000109462Add
    BLAST

    Proteomic databases

    MaxQBiP16658.
    PaxDbiP16658.

    Expressioni

    Gene expression databases

    GenevestigatoriP16658.

    Interactioni

    Subunit structurei

    Heterotetramer composed of SEN2, SEN15, SEN34 and SEN54. Interacts directly with SEN54.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    SEN54Q028254EBI-16953,EBI-16829

    Protein-protein interaction databases

    BioGridi31378. 22 interactions.
    DIPiDIP-4821N.
    IntActiP16658. 4 interactions.
    MINTiMINT-546309.
    STRINGi4932.YLR105C.

    Structurei

    3D structure databases

    ProteinModelPortaliP16658.
    SMRiP16658. Positions 259-332.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili119 – 17456Sequence AnalysisAdd
    BLAST

    Sequence similaritiesi

    Belongs to the tRNA-intron endonuclease family.Curated

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiCOG1676.
    GeneTreeiENSGT00390000013266.
    HOGENOMiHOG000159660.
    KOiK15322.
    OMAiSPACLAH.
    OrthoDBiEOG7SXWFH.

    Family and domain databases

    Gene3Di3.40.1350.10. 1 hit.
    InterProiIPR011856. tRNA_endonuc-like_dom.
    IPR006677. tRNA_intron_Endonuc_cat-like.
    IPR006676. tRNA_splic.
    IPR016589. tRNA_splic_SEN2.
    [Graphical view]
    PfamiPF01974. tRNA_int_endo. 1 hit.
    [Graphical view]
    PIRSFiPIRSF011789. tRNA_splic_SEN2. 1 hit.
    SUPFAMiSSF53032. SSF53032. 1 hit.
    TIGRFAMsiTIGR00324. endA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P16658-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKGRVNQKR YKYPLPIHPV DDLPELILHN PLSWLYWAYR YYKSTNALND    50
    KVHVDFIGDT TLHITVQDDK QMLYLWNNGF FGTGQFSRSE PTWKARTEAR 100
    LGLNDTPLHN RGGTKSNTET EMTLEKVTQQ RRLQRLEFKK ERAKLERELL 150
    ELRKKGGHID EENILLEKQR ESLRKFKLKQ TEDVGIVAQQ QDISESNLRD 200
    EDNNLLDENG DLLPLESLEL MPVEAMFLTF ALPVLDISPA CLAGKLFQFD 250
    AKYKDIHSFV RSYVIYHHYR SHGWCVRSGI KFGCDYLLYK RGPPFQHAEF 300
    CVMGLDHDVS KDYTWYSSIA RVVGGAKKTF VLCYVERLIS EQEAIALWKS 350
    NNFTKLFNSF QVGEVLYKRW VPGRNRD 377
    Length:377
    Mass (Da):44,109
    Last modified:August 1, 1990 - v1
    Checksum:iB5A9C7F865538F5C
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti292 – 2921G → E in the cold-sensitive allele sen2-3; defective in cleavage only at the 5'-splice site of tRNA precursors.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M32336 Genomic DNA. Translation: AAB65811.1.
    Z73277 Genomic DNA. Translation: CAA97670.1.
    U53876 Genomic DNA. Translation: AAB67547.1.
    BK006945 Genomic DNA. Translation: DAA09421.1.
    PIRiA38862.
    RefSeqiNP_013206.1. NM_001181992.1.

    Genome annotation databases

    EnsemblFungiiYLR105C; YLR105C; YLR105C.
    GeneIDi850795.
    KEGGisce:YLR105C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M32336 Genomic DNA. Translation: AAB65811.1 .
    Z73277 Genomic DNA. Translation: CAA97670.1 .
    U53876 Genomic DNA. Translation: AAB67547.1 .
    BK006945 Genomic DNA. Translation: DAA09421.1 .
    PIRi A38862.
    RefSeqi NP_013206.1. NM_001181992.1.

    3D structure databases

    ProteinModelPortali P16658.
    SMRi P16658. Positions 259-332.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31378. 22 interactions.
    DIPi DIP-4821N.
    IntActi P16658. 4 interactions.
    MINTi MINT-546309.
    STRINGi 4932.YLR105C.

    Proteomic databases

    MaxQBi P16658.
    PaxDbi P16658.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YLR105C ; YLR105C ; YLR105C .
    GeneIDi 850795.
    KEGGi sce:YLR105C.

    Organism-specific databases

    CYGDi YLR105c.
    SGDi S000004095. SEN2.

    Phylogenomic databases

    eggNOGi COG1676.
    GeneTreei ENSGT00390000013266.
    HOGENOMi HOG000159660.
    KOi K15322.
    OMAi SPACLAH.
    OrthoDBi EOG7SXWFH.

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-16148.
    YEAST:G3O-32253-MONOMER.

    Miscellaneous databases

    NextBioi 967008.
    PROi P16658.

    Gene expression databases

    Genevestigatori P16658.

    Family and domain databases

    Gene3Di 3.40.1350.10. 1 hit.
    InterProi IPR011856. tRNA_endonuc-like_dom.
    IPR006677. tRNA_intron_Endonuc_cat-like.
    IPR006676. tRNA_splic.
    IPR016589. tRNA_splic_SEN2.
    [Graphical view ]
    Pfami PF01974. tRNA_int_endo. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF011789. tRNA_splic_SEN2. 1 hit.
    SUPFAMi SSF53032. SSF53032. 1 hit.
    TIGRFAMsi TIGR00324. endA. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases."
      Trotta C.R., Miao F., Arn E.A., Stevens S.W., Ho C.K., Rauhut R., Abelson J.N.
      Cell 89:849-858(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION, SUBUNIT, MUTANT SEN2-3.
    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.
      , 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. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Yeast tRNA-splicing endonuclease is a heterotrimeric enzyme."
      Rauhut R., Green P.R., Abelson J.N.
      J. Biol. Chem. 265:18180-18184(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    5. "Accumulation of pre-tRNA splicing '2/3' intermediates in a Saccharomyces cerevisiae mutant."
      Ho C.K., Rauhut R., Vijayraghavan U., Abelson J.
      EMBO J. 9:1245-1252(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. "Possibility of cytoplasmic pre-tRNA splicing: the yeast tRNA splicing endonuclease mainly localizes on the mitochondria."
      Yoshihisa T., Yunoki-Esaki K., Ohshima C., Tanaka N., Endo T.
      Mol. Biol. Cell 14:3266-3279(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSEN2_YEAST
    AccessioniPrimary (citable) accession number: P16658
    Secondary accession number(s): D6VYA5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: August 1, 1990
    Last modified: October 1, 2014
    This is version 137 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The tRNA splicing endonuclease complex is present with 100 molecules/cell.1 Publication
    Present with 319 molecules/cell in log phase SD medium.1 Publication

    Caution

    According to PubMed:9200603, it contains a transmembrane domain and may be responsible to anchor the complex into membranes, however, PubMed:12925762 showed that it is peripherically associated with membranes, and is probably not a transmembrane protein.Curated

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome XII
      Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

    External Data

    Dasty 3