P16658 (SEN2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA-splicing endonuclease subunit SEN2
EC=3.1.27.9

Alternative name(s):
Splicing endonuclease protein 2
tRNA-intron endonuclease SEN2

Gene names

Name:	SEN2
Ordered Locus Names:	YLR105C
ORF Names:	L8004.12

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	377 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron.
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.

Ontologies

Keywords
Biological process	tRNA processing
Cellular component	Membrane Mitochondrion Mitochondrion outer membrane Nucleus
Domain	Coiled coil
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	tRNA-type intron splice site recognition and cleavage Inferred from direct assay Ref.1. Source: SGD
Cellular_component	endomembrane system Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrial outer membrane Inferred from direct assay Ref.6PubMed 16407407. Source: SGD tRNA-intron endonuclease complex Inferred from direct assay Ref.1. Source: SGD
Molecular_function	nucleic acid binding Inferred from electronic annotation. Source: InterPro tRNA-intron endonuclease activity Inferred from direct assay Ref.1. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SEN54	Q02825	4	EBI-16953,EBI-16829

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 377	377	tRNA-splicing endonuclease subunit SEN2		PRO_0000109462
Regions
	Coiled coil	119 – 174	56	Potential
Sites
	Active site	289	1	By similarity
	Active site	297	1	By similarity
	Active site	328	1	By similarity
Natural variations
	Natural variant	292	1	G → E in the cold-sensitive allele sen2-3; defective in cleavage only at the 5'-splice site of tRNA precursors.

Sequences

	Sequence		Length	Mass (Da)
	P16658 [UniParc]. Last modified August 1, 1990. Version 1. Checksum: B5A9C7F865538F5C	FASTA	377	44,109
	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

References

	« Hide 'large scale' referencesShow '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. , 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 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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.
PIR	A38862.
RefSeq	NP_013206.1. NM_001181992.1.
3D structure databases
ProteinModelPortal	P16658.
SMR	P16658. Positions 259-332.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-4821N.
IntAct	P16658. 6 interactions.
MINT	MINT-546309.
STRING	4932.YLR105C.
Proteomic databases
PaxDb	P16658.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YLR105C; YLR105C; YLR105C.
GeneID	850795.
KEGG	sce:YLR105C.
Organism-specific databases
CYGD	YLR105c.
SGD	S000004095. SEN2.
Phylogenomic databases
eggNOG	COG1676.
GeneTree	ENSGT00390000013266.
HOGENOM	HOG000159660.
KO	K15322.
OMA	CVRSGIK.
OrthoDB	EOG4PCF2K.
Enzyme and pathway databases
BioCyc	MetaCyc:MONOMER-16148.
Gene expression databases
Genevestigator	P16658.
GermOnline	YLR105C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.40.1350.10. 1 hit.
InterPro	IPR011856. tRNA_endonuc-like_dom. IPR006677. tRNA_intron_Endonuc_cat-like. IPR006676. tRNA_splic. IPR016589. tRNA_splic_SEN2. [Graphical view]
Pfam	PF01974. tRNA_int_endo. 1 hit. [Graphical view]
PIRSF	PIRSF011789. tRNA_splic_SEN2. 1 hit.
SUPFAM	SSF53032. tRNA_int_endo_C. 1 hit.
TIGRFAMs	TIGR00324. endA. 1 hit.
ProtoNet	Search...
Other
NextBio	967008.

Entry information

Entry name

SEN2_YEAST

Accession

Primary (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:	May 1, 2013
This is version 125 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program