ID   SEN2_ORYSJ              Reviewed;         293 AA.
AC   Q5Z6B1; Q0DBS8;
DT   06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   24-JAN-2024, entry version 101.
DE   RecName: Full=Probable tRNA-splicing endonuclease subunit Sen2;
DE            EC=4.6.1.16;
DE   AltName: Full=tRNA-intron endonuclease Sen2;
GN   OrderedLocusNames=Os06g0530700, LOC_Os06g33980;
GN   ORFNames=P0410C01.17, P0438E12.38;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
CC   -!- FUNCTION: Constitutes one of the two catalytic subunit of the tRNA-
CC       splicing endonuclease complex, a complex responsible for identification
CC       and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at
CC       the 5'- and 3'-splice sites to release the intron. The products are an
CC       intron and two tRNA half-molecules bearing 2',3'-cyclic phosphate and
CC       5'-OH termini. There are no conserved sequences at the splice sites,
CC       but the intron is invariably located at the same site in the gene,
CC       placing the splice sites an invariant distance from the constant
CC       structural features of the tRNA body. Probably carries the active site
CC       for 5'-splice site cleavage (By similarity). {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=pretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-
CC         half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with
CC         a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus.; EC=4.6.1.16;
CC   -!- SUBUNIT: tRNA splicing endonuclease is a heterotetramer composed of
CC       SEN2, SEN15, SEN34/LENG5 and SEN54. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Membrane {ECO:0000305};
CC       Single-pass membrane protein {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the tRNA-intron endonuclease family.
CC       {ECO:0000305}.
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DR   EMBL; AP004749; BAD54220.1; -; Genomic_DNA.
DR   EMBL; AP005450; BAD54480.1; -; Genomic_DNA.
DR   EMBL; AP008212; BAF19695.1; -; Genomic_DNA.
DR   EMBL; AP014962; BAS98061.1; -; Genomic_DNA.
DR   EMBL; AK059057; BAG86882.1; -; mRNA.
DR   EMBL; AK102915; BAG95781.1; -; mRNA.
DR   RefSeq; XP_015641868.1; XM_015786382.1.
DR   RefSeq; XP_015641869.1; XM_015786383.1.
DR   RefSeq; XP_015641870.1; XM_015786384.1.
DR   RefSeq; XP_015641871.1; XM_015786385.1.
DR   AlphaFoldDB; Q5Z6B1; -.
DR   SMR; Q5Z6B1; -.
DR   STRING; 39947.Q5Z6B1; -.
DR   PaxDb; 39947-Q5Z6B1; -.
DR   EnsemblPlants; Os06t0530700-02; Os06t0530700-02; Os06g0530700.
DR   GeneID; 4341203; -.
DR   Gramene; Os06t0530700-02; Os06t0530700-02; Os06g0530700.
DR   KEGG; osa:4341203; -.
DR   eggNOG; KOG4685; Eukaryota.
DR   HOGENOM; CLU_053228_0_0_1; -.
DR   InParanoid; Q5Z6B1; -.
DR   OrthoDB; 35871at2759; -.
DR   Proteomes; UP000000763; Chromosome 6.
DR   Proteomes; UP000059680; Chromosome 6.
DR   ExpressionAtlas; Q5Z6B1; baseline and differential.
DR   GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0000214; C:tRNA-intron endonuclease complex; IBA:GO_Central.
DR   GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR   GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR   GO; GO:0000213; F:tRNA-intron endonuclease activity; IBA:GO_Central.
DR   GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR   GO; GO:0000379; P:tRNA-type intron splice site recognition and cleavage; IBA:GO_Central.
DR   CDD; cd22363; tRNA-intron_lyase_C; 1.
DR   Gene3D; 3.40.1350.10; -; 1.
DR   InterPro; IPR011856; tRNA_endonuc-like_dom_sf.
DR   InterPro; IPR036167; tRNA_intron_Endo_cat-like_sf.
DR   InterPro; IPR006677; tRNA_intron_Endonuc_cat-like.
DR   InterPro; IPR006678; tRNA_intron_Endonuc_N.
DR   InterPro; IPR006676; tRNA_splic.
DR   PANTHER; PTHR21227; TRNA-SPLICING ENDONUCLEASE SUBUNIT SEN2; 1.
DR   PANTHER; PTHR21227:SF0; TRNA-SPLICING ENDONUCLEASE SUBUNIT SEN2; 1.
DR   Pfam; PF01974; tRNA_int_endo; 1.
DR   Pfam; PF02778; tRNA_int_endo_N; 1.
DR   SUPFAM; SSF53032; tRNA-intron endonuclease catalytic domain-like; 1.
DR   Genevisible; Q5Z6B1; OS.
PE   2: Evidence at transcript level;
KW   Lyase; Membrane; mRNA processing; Nucleus; Reference proteome;
KW   Transmembrane; Transmembrane helix; tRNA processing.
FT   CHAIN           1..293
FT                   /note="Probable tRNA-splicing endonuclease subunit Sen2"
FT                   /id="PRO_0000109458"
FT   TRANSMEM        267..287
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        157
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        165
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        204
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   293 AA;  32737 MW;  673DE4101F5408C1 CRC64;
     MDLPGPRWKK GKDGKDFASL AAANPMSAIV SELKASFISS KPVAILSGPG GSAVLGVGPE
     QAVILNRAAF GHAIENATAQ KHWFQLSPEE VFYLCHALNC IRVDSLDNKQ MSEIELWDYF
     RSGSESFPEM YKAYAHLRLK NWVVRSGLQY GADFVAYRHH PALVHSEFAV VVVPEGAEFG
     NRCGRLEVWS DLLCALRASG SVAKTLLVLT ISSSSKCELS SPDCLEQLVV HERTITRWIL
     QQCREQRCEP SRDEVNREEL IIEKESVVFN HWGVILGFTV LSGLLVYRLK FRQ
//