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P16658

- SEN2_YEAST

UniProt

P16658 - SEN2_YEAST

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Protein
tRNA-splicing endonuclease subunit SEN2
Gene
SEN2, YLR105C, L8004.12
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 – 2891 By similarity
Active sitei297 – 2971 By similarity
Active sitei328 – 3281 By 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
Complete GO annotation...

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. Endomembrane system; Peripheral membrane protein. Mitochondrion outer membrane; Peripheral membrane protein; Cytoplasmic side
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.1 Publication

GO - Cellular componenti

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

Keywords - Cellular componenti

Membrane, Mitochondrion, Mitochondrion outer membrane, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 377377tRNA-splicing endonuclease subunit SEN2
PRO_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.

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili119 – 17456 Reviewed prediction
Add
BLAST

Sequence similaritiesi

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

« Hide 'large scale' publications
  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: June 11, 2014
This is version 136 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.
Present with 319 molecules/cell in log phase SD medium.

Caution

According to 1 Publication, it contains a transmembrane domain and may be responsible to anchor the complex into membranes, however, 1 Publication showed that it is peripherically associated with membranes, and is probably not a transmembrane protein.

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

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