Q9BSV6 (SEN34_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA-splicing endonuclease subunit Sen34
EC=3.1.27.9

Alternative name(s):
Leukocyte receptor cluster member 5
tRNA-intron endonuclease Sen34
Short name=HsSen34

Gene names

Name:	TSEN34
Synonyms:	LENG5, SEN34

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	310 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. It probably carries the active site for 3'-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. Ref.1
Catalytic activity	Endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron.
Subunit structure	tRNA splicing endonuclease is a heterotetramer composed of SEN2, SEN15, SEN34/LENG5 and SEN54. tRNA splicing endonuclease complex also contains proteins of the pre-mRNA 3'-end processing machinery such as CLP1, CPSF1, CPSF4 and CSTF2. Ref.6
Subcellular location	Nucleus. Nucleus › nucleolus. Note: May be transiently localized in the nucleolus. Ref.1
Involvement in disease	Pontocerebellar hypoplasia 2C (PCH2C) [MIM:612390]: A 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. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.9
Miscellaneous	Belongs to the leukocyte receptor cluster (LRC) present on 19q13.4.
Sequence similarities	Belongs to the tRNA-intron endonuclease family.
Sequence caution	The sequence BAB15284.1 differs from that shown. Reason: Erroneous termination at position 311. Translated as stop.

Ontologies

Keywords
Biological process	mRNA processing tRNA processing
Cellular component	Nucleus
Coding sequence diversity	Polymorphism
Disease	Disease mutation Pontocerebellar hypoplasia
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC tRNA-type intron splice site recognition and cleavage Inferred from electronic annotation. Source: InterPro
Cellular_component	nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell tRNA-intron endonuclease complex Inferred from electronic annotation. Source: InterPro
Molecular_function	nucleic acid binding Inferred from electronic annotation. Source: InterPro tRNA-intron endonuclease activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 310	310	tRNA-splicing endonuclease subunit Sen34		PRO_0000109463
Sites
	Active site	247	1	By similarity
	Active site	255	1	By similarity
	Active site	286	1	By similarity
Natural variations
	Natural variant	58	1	R → W in PCH2C. Ref.9		VAR_054811
	Natural variant	112	1	L → V. Ref.2 Corresponds to variant rs17849378 [ dbSNP | Ensembl ].		VAR_061149

Sequences

	Sequence		Length	Mass (Da)
	Q9BSV6 [UniParc]. Last modified June 1, 2001. Version 1. Checksum: 1C1522D030148EC3	FASTA	310	33,652
	10 20 30 40 50 60 MLVVEVANGR SLVWGAEAVQ ALRERLGVGG RTVGALPRGP RQNSRLGLPL LLMPEEARLL 70 80 90 100 110 120 AEIGAVTLVS APRPDSRHHS LALTSFKRQQ EESFQEQSAL AAEARETRRQ ELLEKITEGQ 130 140 150 160 170 180 AAKKQKLEQA SGASSSQEAG SSQAAKEDET SDGQASGEQE EAGPSSSQAG PSNGVAPLPR 190 200 210 220 230 240 SALLVQLATA RPRPVKARPL DWRVQSKDWP HAGRPAHELR YSIYRDLWER GFFLSAAGKF 250 260 270 280 290 300 GGDFLVYPGD PLRFHAHYIA QCWAPEDTIP LQDLVAAGRL GTSVRKTLLL CSPQPDGKVV 310 YTSLQWASLQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation." Paushkin S.V., Patel M., Furia B.S., Peltz S.W., Trotta C.R. Cell 117:311-321(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, COMPONENT OF A COMPLEX WITH SEN2; SEN15; SEN54 AND CLP1.
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT VAL-112. Tissue: Kidney epithelium.
[3]	"The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M. Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Brain and Eye.
[6]	"Extensive gene duplications and a large inversion characterize the human leukocyte receptor cluster." Wende H., Volz A., Ziegler A. Immunogenetics 51:703-713(2000) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE LRC.
[7]	Erratum Wende H., Volz A., Ziegler A. Immunogenetics 52:3-4(2001)
[8]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]	"tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia." Budde B.S., Namavar Y., Barth P.G., Poll-The B.T., Nuernberg G., Becker C., van Ruissen F., Weterman M.A.J., Fluiter K., te Beek E.T., Aronica E., van der Knaap M.S., Hoehne W., Toliat M.R., Crow Y.J., Steinling M., Voit T., Roelenso F. , Brussel W., Brockmann K., Kyllerman M., Boltshauser E., Hammersen G., Willemsen M., Basel-Vanagaite L., Kraegeloh-Mann I., de Vries L.S., Sztriha L., Muntoni F., Ferrie C.D., Battini R., Hennekam R.C.M., Grillo E., Beemer F.A., Stoets L.M.E., Wollnik B., Nuernberg P., Baas F. Nat. Genet. 40:1113-1118(2008) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT PCH2C TRP-58.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AK025929 mRNA. Translation: BAB15284.1. Sequence problems. CU457734 Genomic DNA. Translation: CAP19124.1. CU151838 Genomic DNA. Translation: CAQ09596.1. CH471135 Genomic DNA. Translation: EAW72203.1. BC004530 mRNA. Translation: AAH04530.1. BC020805 mRNA. Translation: AAH20805.1.
IPI	IPI00940410.
RefSeq	NP_001070914.1. NM_001077446.2. NP_076980.2. NM_024075.3.
UniGene	Hs.15580.
3D structure databases
ProteinModelPortal	Q9BSV6.
ModBase	Search...
Protein-protein interaction databases
STRING	9606.ENSP00000305524.
PTM databases
PhosphoSite	Q9BSV6.
Polymorphism databases
DMDM	50401668.
Proteomic databases
PaxDb	Q9BSV6.
PeptideAtlas	Q9BSV6.
PRIDE	Q9BSV6.
Protocols and materials databases
DNASU	79042.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000302937; ENSP00000305524; ENSG00000170892. ENST00000396383; ENSP00000379667; ENSG00000170892. ENST00000396388; ENSP00000379671; ENSG00000170892. ENST00000571364; ENSP00000460819; ENSG00000269366. ENST00000571677; ENSP00000460904; ENSG00000262716. ENST00000572746; ENSP00000459858; ENSG00000269366. ENST00000572922; ENSP00000458776; ENSG00000262868. ENST00000573330; ENSP00000458839; ENSG00000262868. ENST00000573700; ENSP00000458617; ENSG00000262716. ENST00000574141; ENSP00000458732; ENSG00000262868. ENST00000575240; ENSP00000460175; ENSG00000269366. ENST00000575967; ENSP00000461803; ENSG00000262716. ENST00000593507; ENSP00000470873; ENSG00000268973. ENST00000595421; ENSP00000468875; ENSG00000269221. ENST00000596846; ENSP00000471329; ENSG00000269221. ENST00000597794; ENSP00000472494; ENSG00000268588. ENST00000597962; ENSP00000471027; ENSG00000268588. ENST00000598602; ENSP00000471526; ENSG00000267903. ENST00000598883; ENSP00000472812; ENSG00000269221. ENST00000599816; ENSP00000469088; ENSG00000268562. ENST00000600050; ENSP00000471673; ENSG00000267903. ENST00000600856; ENSP00000469743; ENSG00000267903. ENST00000600870; ENSP00000471131; ENSG00000268562. ENST00000601055; ENSP00000472149; ENSG00000268562. ENST00000601153; ENSP00000471282; ENSG00000268973. ENST00000601248; ENSP00000469131; ENSG00000268973. ENST00000601721; ENSP00000470924; ENSG00000268588.
GeneID	79042.
KEGG	hsa:79042.
UCSC	uc002qdu.3. human.
Organism-specific databases
CTD	79042.
GeneCards	GC19P054834.
HGNC	HGNC:15506. TSEN34.
HPA	HPA041111.
MIM	608754. gene. 612390. phenotype.
neXtProt	NX_Q9BSV6.
Orphanet	2524. Pontocerebellar hypoplasia type 2.
PharmGKB	PA134871088.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG1676.
HOGENOM	HOG000232197.
HOVERGEN	HBG054846.
InParanoid	Q9BSV6.
KO	K15323.
OrthoDB	EOG479F7J.
Gene expression databases
ArrayExpress	Q9BSV6.
Bgee	Q9BSV6.
CleanEx	HS_TSEN34.
Genevestigator	Q9BSV6.
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. IPR016690. tRNA_splic_SEN34. [Graphical view]
Pfam	PF01974. tRNA_int_endo. 1 hit. [Graphical view]
PIRSF	PIRSF017250. tRNA_splic_SEN34. 1 hit.
SUPFAM	SSF53032. tRNA_int_endo_C. 1 hit.
TIGRFAMs	TIGR00324. endA. 1 hit.
ProtoNet	Search...
Other
GenomeRNAi	79042.
NextBio	67781.
SOURCE	Search...

Entry information

Entry name

SEN34_HUMAN

Accession

Primary (citable) accession number: Q9BSV6
Secondary accession number(s): A6NNB1 , B0V3J1, Q9BVT1, Q9H6H5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	June 1, 2001
Last modified:	May 1, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.