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P16658 (SEN2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 136. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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:
tRNA-splicing endonuclease subunit SEN2

EC=4.6.1.16
Alternative name(s):
Splicing endonuclease protein 2
tRNA-intron endonuclease SEN2
Gene names
Name:SEN2
Ordered Locus Names:YLR105C
ORF Names:L8004.12
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length377 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5

Catalytic activity

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.

Subunit structure

Heterotetramer composed of SEN2, SEN15, SEN34 and SEN54. Interacts directly with SEN54. Ref.1 Ref.4

Subcellular location

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. Ref.6

Miscellaneous

The tRNA splicing endonuclease complex is present with 100 molecules/cell.

Present with 319 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the tRNA-intron endonuclease family.

Caution

According to Ref.1, it contains a transmembrane domain and may be responsible to anchor the complex into membranes, however, Ref.6 showed that it is peripherically associated with membranes, and is probably not a transmembrane protein.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

SEN54Q028254EBI-16953,EBI-16829

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 377377tRNA-splicing endonuclease subunit SEN2
PRO_0000109462

Regions

Coiled coil119 – 17456 Potential

Sites

Active site2891 By similarity
Active site2971 By similarity
Active site3281 By similarity

Natural variations

Natural variant2921G → E in the cold-sensitive allele sen2-3; defective in cleavage only at the 5'-splice site of tRNA precursors.

Sequences

Sequence LengthMass (Da)Tools
P16658 [UniParc].

Last modified August 1, 1990. Version 1.
Checksum: B5A9C7F865538F5C

FASTA37744,109
        10         20         30         40         50         60 
MSKGRVNQKR YKYPLPIHPV DDLPELILHN PLSWLYWAYR YYKSTNALND KVHVDFIGDT 

        70         80         90        100        110        120 
TLHITVQDDK QMLYLWNNGF FGTGQFSRSE PTWKARTEAR LGLNDTPLHN RGGTKSNTET 

       130        140        150        160        170        180 
EMTLEKVTQQ RRLQRLEFKK ERAKLERELL ELRKKGGHID EENILLEKQR ESLRKFKLKQ 

       190        200        210        220        230        240 
TEDVGIVAQQ QDISESNLRD EDNNLLDENG DLLPLESLEL MPVEAMFLTF ALPVLDISPA 

       250        260        270        280        290        300 
CLAGKLFQFD AKYKDIHSFV RSYVIYHHYR SHGWCVRSGI KFGCDYLLYK RGPPFQHAEF 

       310        320        330        340        350        360 
CVMGLDHDVS KDYTWYSSIA RVVGGAKKTF VLCYVERLIS EQEAIALWKS NNFTKLFNSF 

       370 
QVGEVLYKRW VPGRNRD 

« Hide

References

« Hide 'large scale' references
[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. 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]"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]"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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M32336 Genomic DNA. Translation: AAB65811.1.
Z73277 Genomic DNA. Translation: CAA97670.1.
U53876 Genomic DNA. Translation: AAB67547.1.
BK006945 Genomic DNA. Translation: DAA09421.1.
PIRA38862.
RefSeqNP_013206.1. NM_001181992.1.

3D structure databases

ProteinModelPortalP16658.
SMRP16658. Positions 259-332.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31378. 22 interactions.
DIPDIP-4821N.
IntActP16658. 4 interactions.
MINTMINT-546309.
STRING4932.YLR105C.

Proteomic databases

MaxQBP16658.
PaxDbP16658.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYLR105C; YLR105C; YLR105C.
GeneID850795.
KEGGsce:YLR105C.

Organism-specific databases

CYGDYLR105c.
SGDS000004095. SEN2.

Phylogenomic databases

eggNOGCOG1676.
GeneTreeENSGT00390000013266.
HOGENOMHOG000159660.
KOK15322.
OMASPACLAH.
OrthoDBEOG7SXWFH.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP16658.

Family and domain databases

Gene3D3.40.1350.10. 1 hit.
InterProIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006676. tRNA_splic.
IPR016589. tRNA_splic_SEN2.
[Graphical view]
PfamPF01974. tRNA_int_endo. 1 hit.
[Graphical view]
PIRSFPIRSF011789. tRNA_splic_SEN2. 1 hit.
SUPFAMSSF53032. SSF53032. 1 hit.
TIGRFAMsTIGR00324. endA. 1 hit.
ProtoNetSearch...

Other

NextBio967008.
PROP16658.

Entry information

Entry nameSEN2_YEAST
AccessionPrimary (citable) accession number: P16658
Secondary accession number(s): D6VYA5
Entry history
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 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