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UniProtKB - Q8NCE0 (SEN2_HUMAN)

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Protein

tRNA-splicing endonuclease subunit Sen2

Gene

TSEN2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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. Isoform 1 probably carries the active site for 5'-splice site cleavage. The tRNA splicing endonuclease is also involved in mRNA processing via its association with pre-mRNA 3'-end processing factors, establishing a link between pre-tRNA splicing and pre-mRNA 3'-end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events. Isoform 2 is responsible for processing a yet unknown RNA substrate. The complex containing isoform 2 is not able to cleave pre-tRNAs properly, although it retains endonucleolytic activity.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)DescriptionActionsGraphical viewLength
Active sitei369By similarity1
Active sitei377By similarity1
Active sitei416By similarity1

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionLyase
Biological processmRNA processing, tRNA processing

Enzyme and pathway databases

BioCyciMetaCyc:HS08007-MONOMER
ReactomeiR-HSA-6784531 tRNA processing in the nucleus

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing endonuclease subunit Sen2 (EC:4.6.1.16)
Alternative name(s):
tRNA-intron endonuclease Sen2
Short name:
HsSen2
Gene namesi
Name:TSEN2
Synonyms:SEN2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000154743.17
HGNCiHGNC:28422 TSEN2
MIMi608753 gene
neXtProtiNX_Q8NCE0

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Pontocerebellar hypoplasia 2B (PCH2B)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by an abnormally small cerebellum and brainstem, and progressive microcephaly from birth combined with extrapyramidal dyskinesia. Severe chorea occurs and epilepsy is frequent. There are no signs of spinal cord anterior horn cells degeneration.
See also OMIM:612389
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_054810309Y → C in PCH2B. 1 PublicationCorresponds to variant dbSNP:rs113994149EnsemblClinVar.1

Keywords - Diseasei

Neurodegeneration, Pontocerebellar hypoplasia

Organism-specific databases

DisGeNETi80746
MalaCardsiTSEN2
MIMi612389 phenotype
OpenTargetsiENSG00000154743
Orphaneti2524 Pontocerebellar hypoplasia type 2
PharmGKBiPA142670695

Polymorphism and mutation databases

BioMutaiTSEN2
DMDMi50428914

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001094521 – 465tRNA-splicing endonuclease subunit Sen2Add BLAST465

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei408PhosphoserineBy similarity1
Modified residuei411PhosphoserineBy similarity1
Modified residuei415PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8NCE0
MaxQBiQ8NCE0
PaxDbiQ8NCE0
PeptideAtlasiQ8NCE0
PRIDEiQ8NCE0
ProteomicsDBi72878
72879 [Q8NCE0-2]
72880 [Q8NCE0-3]

PTM databases

iPTMnetiQ8NCE0
PhosphoSitePlusiQ8NCE0

Expressioni

Tissue specificityi

Isoform 1 and isoform 2 are widely expressed at very low level.1 Publication

Gene expression databases

BgeeiENSG00000154743
CleanExiHS_TSEN2
ExpressionAtlasiQ8NCE0 baseline and differential
GenevisibleiQ8NCE0 HS

Organism-specific databases

HPAiHPA027120
HPA027125
HPA027268

Interactioni

Subunit structurei

tRNA splicing endonuclease is a heterotetramer composed of isoform 1 of TSEN2, TSEN15, TSEN34/LENG5 and TSEN54. tRNA splicing endonuclease complex also contains proteins of the pre-mRNA 3'-end processing machinery such as CLP1, CPSF1, CPSF4 and CSTF2. Isoform 2 belongs to a different complex that contains TSEN54 but low level of TSEN15 and TSEN34/LENG5.

Binary interactionsi

WithEntry#Exp.IntActNotes
TSEN54Q7Z6J97EBI-2559818,EBI-2559824

Protein-protein interaction databases

BioGridi123288, 31 interactors
CORUMiQ8NCE0
IntActiQ8NCE0, 9 interactors
STRINGi9606.ENSP00000284995

Structurei

3D structure databases

ProteinModelPortaliQ8NCE0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the tRNA-intron endonuclease family.Curated

Phylogenomic databases

eggNOGiKOG4685 Eukaryota
COG1676 LUCA
GeneTreeiENSGT00390000013266
HOGENOMiHOG000154285
HOVERGENiHBG056610
InParanoidiQ8NCE0
KOiK15322
OrthoDBiEOG091G0FMD
PhylomeDBiQ8NCE0
TreeFamiTF314679

Family and domain databases

Gene3Di3.40.1350.10, 1 hit
InterProiView protein in InterPro
IPR011856 tRNA_endonuc-like_dom_sf
IPR036167 tRNA_intron_Endo_cat-like_sf
IPR006677 tRNA_intron_Endonuc_cat-like
IPR006678 tRNA_intron_Endonuc_N
IPR006676 tRNA_splic
IPR016589 tRNA_splic_SEN2
PANTHERiPTHR21227 PTHR21227, 1 hit
PfamiView protein in Pfam
PF01974 tRNA_int_endo, 1 hit
PF02778 tRNA_int_endo_N, 1 hit
PIRSFiPIRSF011789 tRNA_splic_SEN2, 1 hit
SUPFAMiSSF53032 SSF53032, 1 hit

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8NCE0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAEAVFHAPK RKRRVYETYE SPLPIPFGQD HGPLKEFKIF RAEMINNNVI 
        60         70         80         90        100
VRNAEDIEQL YGKGYFGKGI LSRSRPSFTI SDPKLVAKWK DMKTNMPIIT 
       110        120        130        140        150
SKRYQHSVEW AAELMRRQGQ DESTVRRILK DYTKPLEHPP VKRNEEAQVH 
       160        170        180        190        200
DKLNSGMVSN MEGTAGGERP SVVNGDSGKS GGVGDPREPL GCLQEGSGCH 
       210        220        230        240        250
PTTESFEKSV REDASPLPHV CCCKQDALIL QRGLHHEDGS QHIGLLHPGD 
       260        270        280        290        300
RGPDHEYVLV EEAECAMSER EAAPNEELVQ RNRLICRRNP YRIFEYLQLS 
       310        320        330        340        350
LEEAFFLVYA LGCLSIYYEK EPLTIVKLWK AFTVVQPTFR TTYMAYHYFR 
       360        370        380        390        400
SKGWVPKVGL KYGTDLLLYR KGPPFYHASY SVIIELVDDH FEGSLRRPLS 
       410        420        430        440        450
WKSLAALSRV SVNVSKELML CYLIKPSTMT DKEMESPECM KRIKVQEVIL 
       460 
SRWVSSRERS DQDDL
Length:465
Mass (Da):53,247
Last modified:July 19, 2004 - v2
Checksum:iFF523229B05A1345
GO
Isoform 2 (identifier: Q8NCE0-2) [UniParc]FASTAAdd to basket
Also known as: SEN2deltaEx8, DeltaEx8

The sequence of this isoform differs from the canonical sequence as follows:
     304-320: Missing.

Show »
Length:448
Mass (Da):51,265
Checksum:iB616BDFCDA590E32
GO
Isoform 3 (identifier: Q8NCE0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     278-303: Missing.

Note: No experimental confirmation available.
Show »
Length:439
Mass (Da):49,942
Checksum:i97A9E847199BDE08
GO
Isoform 4 (identifier: Q8NCE0-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     173-231: Missing.

Note: No experimental confirmation available.
Show »
Length:406
Mass (Da):47,124
Checksum:i61FD06EBE21EEEFD
GO
Isoform 5 (identifier: Q8NCE0-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     276-301: Missing.
     417-465: ELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL → VTQHQLCHWSVT

Note: No experimental confirmation available.
Show »
Length:402
Mass (Da):45,532
Checksum:i8B231F84B72FA227
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti138H → Q in BAH13287 (PubMed:14702039).Curated1
Sequence conflicti208K → E in BAH13287 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04893141R → H. Corresponds to variant dbSNP:rs12495784EnsemblClinVar.1
Natural variantiVAR_048932126R → H. Corresponds to variant dbSNP:rs33955793EnsemblClinVar.1
Natural variantiVAR_054810309Y → C in PCH2B. 1 PublicationCorresponds to variant dbSNP:rs113994149EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_046192173 – 231Missing in isoform 4. 1 PublicationAdd BLAST59
Alternative sequenceiVSP_046193276 – 301Missing in isoform 5. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_010985278 – 303Missing in isoform 3. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_010986304 – 320Missing in isoform 2. 1 PublicationAdd BLAST17
Alternative sequenceiVSP_046194417 – 465ELMLC…DQDDL → VTQHQLCHWSVT in isoform 5. 1 PublicationAdd BLAST49

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK074794 mRNA Translation: BAC11213.1
AK300449 mRNA Translation: BAH13287.1
AK225875 mRNA No translation available.
AC018500 Genomic DNA No translation available.
AC090947 Genomic DNA No translation available.
CH471055 Genomic DNA Translation: EAW64129.1
BC004178 mRNA Translation: AAH04178.1
BC004211 mRNA Translation: AAH04211.1
BC019582 mRNA Translation: AAH19582.1
BC021975 mRNA Translation: AAH21975.2
CCDSiCCDS2611.1 [Q8NCE0-1]
CCDS46757.1 [Q8NCE0-3]
CCDS46758.1 [Q8NCE0-4]
RefSeqiNP_001138864.1, NM_001145392.1 [Q8NCE0-1]
NP_001138865.1, NM_001145393.2 [Q8NCE0-3]
NP_001138866.1, NM_001145394.1 [Q8NCE0-4]
NP_001308206.1, NM_001321277.1 [Q8NCE0-1]
NP_001308207.1, NM_001321278.1
NP_001308208.1, NM_001321279.1 [Q8NCE0-3]
NP_079541.1, NM_025265.3 [Q8NCE0-1]
XP_016862785.1, XM_017007296.1 [Q8NCE0-1]
UniGeneiHs.335550
Hs.670039

Genome annotation databases

EnsembliENST00000284995; ENSP00000284995; ENSG00000154743 [Q8NCE0-1]
ENST00000402228; ENSP00000385976; ENSG00000154743 [Q8NCE0-1]
ENST00000415684; ENSP00000416510; ENSG00000154743 [Q8NCE0-3]
ENST00000444864; ENSP00000407974; ENSG00000154743 [Q8NCE0-5]
ENST00000454502; ENSP00000392029; ENSG00000154743 [Q8NCE0-4]
GeneIDi80746
KEGGihsa:80746
UCSCiuc003bwz.4 human [Q8NCE0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiSEN2_HUMAN
AccessioniPrimary (citable) accession number: Q8NCE0
Secondary accession number(s): B7Z6K1
, C9IZI7, G5E9Q3, Q8WTW7, Q9BPU7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: June 20, 2018
This is version 136 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

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