ENDA_AERPE
ID ENDA_AERPE Reviewed; 186 AA.
AC Q9YBF1;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 26-JUN-2007, sequence version 2.
DT 03-AUG-2022, entry version 102.
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=APE_1646.1;
OS Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 /
OS K1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Aeropyrum.
OX NCBI_TaxID=272557;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX PubMed=10382966; DOI=10.1093/dnares/6.2.83;
RA Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K.,
RA Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A.,
RA Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S.,
RA Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
RA Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H.;
RT "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon,
RT Aeropyrum pernix K1.";
RL DNA Res. 6:83-101(1999).
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; BA000002; BAA80647.2; -; Genomic_DNA.
DR PIR; B72545; B72545.
DR PDB; 3AJV; X-ray; 1.70 A; B/D=1-186.
DR PDB; 3P1Y; X-ray; 2.05 A; A/B/C/D=39-53.
DR PDB; 3P1Z; X-ray; 2.80 A; B/D/F/H/J/L=1-186.
DR PDBsum; 3AJV; -.
DR PDBsum; 3P1Y; -.
DR PDBsum; 3P1Z; -.
DR AlphaFoldDB; Q9YBF1; -.
DR SMR; Q9YBF1; -.
DR STRING; 272557.APE_1646.1; -.
DR EnsemblBacteria; BAA80647; BAA80647; APE_1646.1.
DR KEGG; ape:APE_1646.1; -.
DR PATRIC; fig|272557.25.peg.1110; -.
DR eggNOG; arCOG01701; Archaea.
DR BRENDA; 4.6.1.16; 171.
DR EvolutionaryTrace; Q9YBF1; -.
DR Proteomes; UP000002518; 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 PANTHER; PTHR21227; PTHR21227; 1.
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..186
FT /note="tRNA-splicing endonuclease"
FT /id="PRO_0000109469"
FT ACT_SITE 125
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01833"
FT ACT_SITE 133
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01833"
FT ACT_SITE 164
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01833"
FT STRAND 10..15
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 18..21
FT /evidence="ECO:0007829|PDB:3AJV"
FT HELIX 24..32
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 54..57
FT /evidence="ECO:0007829|PDB:3AJV"
FT HELIX 58..66
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:3AJV"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:3AJV"
FT HELIX 93..107
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:3AJV"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 120..127
FT /evidence="ECO:0007829|PDB:3AJV"
FT TURN 129..131
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 136..141
FT /evidence="ECO:0007829|PDB:3AJV"
FT HELIX 150..159
FT /evidence="ECO:0007829|PDB:3AJV"
FT TURN 160..162
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 164..172
FT /evidence="ECO:0007829|PDB:3AJV"
FT STRAND 175..183
FT /evidence="ECO:0007829|PDB:3AJV"
SQ SEQUENCE 186 AA; 20602 MW; 3377457A91F479B9 CRC64;
MGDRCAPIKA SGVLIGDSVL VTDVEQARSL YSCGYYGQPL DVEKPRGADF EGPLRLSLIE
SLYLAEKGVL EVAKPDGSSV GVEDLRTAVR GNPRFSMLYN IYRDLRERGF VVRSGLKFGS
DFAVYRLGPG IDHAPFIVHA YSPEDNIDPV EIVRAGRLSH SVRKKFVFAV TRGGDVSYLM
IDWFRP
