ID   ENDA_NANEQ              Reviewed;         154 AA.
AC   Q74MP4;
DT   11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 91.
DE   RecName: Full=tRNA-splicing endonuclease {ECO:0000255|HAMAP-Rule:MF_01833};
DE            EC=4.6.1.16 {ECO:0000255|HAMAP-Rule:MF_01833};
DE   AltName: Full=tRNA-intron endonuclease {ECO:0000255|HAMAP-Rule:MF_01833};
GN   Name=endA {ECO:0000255|HAMAP-Rule:MF_01833}; OrderedLocusNames=NEQ205;
OS   Nanoarchaeum equitans (strain Kin4-M).
OC   Archaea; Nanoarchaeota; Candidatus Nanoarchaeia; Nanoarchaeales;
OC   Nanoarchaeaceae; Nanoarchaeum.
OX   NCBI_TaxID=228908;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Kin4-M;
RX   PubMed=14566062; DOI=10.1073/pnas.1735403100;
RA   Waters E., Hohn M.J., Ahel I., Graham D.E., Adams M.D., Barnstead M.,
RA   Beeson K.Y., Bibbs L., Bolanos R., Keller M., Kretz K., Lin X., Mathur E.,
RA   Ni J., Podar M., Richardson T., Sutton G.G., Simon M., Soell D.,
RA   Stetter K.O., Short J.M., Noorderwier M.;
RT   "The genome of Nanoarchaeum equitans: insights into early archaeal
RT   evolution and derived parasitism.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:12984-12988(2003).
CC   -!- FUNCTION: Endonuclease that removes tRNA introns. 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. Recognizes a pseudosymmetric substrate in which 2 bulged
CC       loops of 3 bases are separated by a stem of 4 bp. {ECO:0000255|HAMAP-
CC       Rule:MF_01833}.
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         Evidence={ECO:0000255|HAMAP-Rule:MF_01833};
CC   -!- SUBUNIT: Homotetramer; although the tetramer contains four active
CC       sites, only two participate in the cleavage. Therefore, it should be
CC       considered as a dimer of dimers. {ECO:0000255|HAMAP-Rule:MF_01833}.
CC   -!- SIMILARITY: Belongs to the tRNA-intron endonuclease family. Archaeal
CC       short subfamily. {ECO:0000255|HAMAP-Rule:MF_01833}.
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DR   EMBL; AE017199; AAR39058.1; -; Genomic_DNA.
DR   PDB; 3IEY; X-ray; 2.11 A; A=1-154.
DR   PDBsum; 3IEY; -.
DR   AlphaFoldDB; Q74MP4; -.
DR   SMR; Q74MP4; -.
DR   STRING; 228908.NEQ205; -.
DR   EnsemblBacteria; AAR39058; AAR39058; NEQ205.
DR   KEGG; neq:NEQ205; -.
DR   HOGENOM; CLU_114393_0_0_2; -.
DR   OMA; KGPGIDH; -.
DR   BRENDA; 4.6.1.16; 8261.
DR   EvolutionaryTrace; Q74MP4; -.
DR   Proteomes; UP000000578; Chromosome.
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; IEA:UniProtKB-UniRule.
DR   GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.40.1350.10; -; 1.
DR   HAMAP; MF_01833; EndA_short; 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; IPR036740; tRNA_intron_Endonuc_N_sf.
DR   InterPro; IPR006676; tRNA_splic.
DR   InterPro; IPR016442; tRNA_splic_arch_short.
DR   Pfam; PF01974; tRNA_int_endo; 1.
DR   Pfam; PF02778; tRNA_int_endo_N; 1.
DR   PIRSF; PIRSF005285; tRNA_splic_archaea; 1.
DR   SUPFAM; SSF53032; SSF53032; 1.
DR   SUPFAM; SSF55267; SSF55267; 1.
DR   TIGRFAMs; TIGR00324; endA; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Lyase; Reference proteome; tRNA processing.
FT   CHAIN           1..154
FT                   /note="tRNA-splicing endonuclease"
FT                   /id="PRO_0000109474"
FT   ACT_SITE        86
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01833"
FT   ACT_SITE        102
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01833"
FT   ACT_SITE        133
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01833"
FT   STRAND          4..6
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   STRAND          9..11
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   HELIX           19..28
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   HELIX           43..52
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   HELIX           56..68
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   STRAND          72..76
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   HELIX           77..79
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   STRAND          81..86
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   TURN            94..96
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   STRAND          99..102
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   STRAND          106..111
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   STRAND          115..117
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   HELIX           118..130
FT                   /evidence="ECO:0007829|PDB:3IEY"
FT   STRAND          135..152
FT                   /evidence="ECO:0007829|PDB:3IEY"
SQ   SEQUENCE   154 AA;  18254 MW;  AFC04DE8E9F9061E CRC64;
     MIGYLFGNRV LVDDKELPLI EAYYLLDKGE LEVYEDDKKL SKEEFLKKCL TYDERFLIRY
     KAYKELRDKG YTLGTALKFG ADFRVYDIGV IPKKGKRSER EHSKWVLYPV SKDETFDFYE
     FASKNRVAHS TRKKLLLGIV SDKIEFIEVS WKKP