TRNL_YEAST
ID TRNL_YEAST Reviewed; 827 AA.
AC P09880; D6VW97;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=tRNA ligase;
DE EC=6.5.1.3 {ECO:0000305};
GN Name=TRL1; Synonyms=RLG1; OrderedLocusNames=YJL087C; ORFNames=J0927;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3277966; DOI=10.1016/s0021-9258(18)69050-7;
RA Westaway S.K., Phizicky E.M., Abelson J.;
RT "Structure and function of the yeast tRNA ligase gene.";
RL J. Biol. Chem. 263:3171-3176(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7483841; DOI=10.1002/yea.320110709;
RA Miosga T., Schaaff-Gerstenschlaeger I., Chalwatzis N., Baur A., Boles E.,
RA Fournier C., Schmitt S., Velten C., Wilhelm N., Zimmermann F.K.;
RT "Sequence analysis of a 33.1 kb fragment from the left arm of Saccharomyces
RT cerevisiae chromosome X, including putative proteins with leucine zippers,
RT a fungal Zn(II)2-Cys6 binuclear cluster domain and a putative alpha 2-SCB-
RT alpha 2 binding site.";
RL Yeast 11:681-689(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP ACTIVE SITE.
RX PubMed=2207062; DOI=10.1021/bi00478a004;
RA Xu Q., Teplow D., Lee T.D., Abelson J.;
RT "Domain structure in yeast tRNA ligase.";
RL Biochemistry 29:6132-6138(1990).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
CC -!- FUNCTION: One of the two proteins required for the splicing of
CC precursor tRNA molecules containing introns. The ligation activity
CC requires three enzymatic activities: phosphorylation of the 5' terminus
CC of the 3' half-tRNA in the presence of ATP, opening of the 2'3'-cyclic
CC phosphodiester bond of the 5' half-tRNA leaving a 2'-phosphomonoester
CC and ligation of the two tRNA halves in an ATP-dependent reaction.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.;
CC EC=6.5.1.3; Evidence={ECO:0000305};
CC -!- DOMAIN: Has three domains each corresponding to an enzymatic activity,
CC namely in N- to C-terminal order: ligase, kinase and cyclic
CC phosphodiesterase (CPDase).
CC -!- MISCELLANEOUS: tRNA ligase is a relatively rare protein with about 400
CC copies per yeast cell.
CC -!- MISCELLANEOUS: Present with 3110 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the TRL1 family. {ECO:0000305}.
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DR EMBL; J03546; AAA66921.1; -; Genomic_DNA.
DR EMBL; X83502; CAA58482.1; -; Genomic_DNA.
DR EMBL; Z49362; CAA89378.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08713.1; -; Genomic_DNA.
DR PIR; A29917; A29917.
DR RefSeq; NP_012448.1; NM_001181520.1.
DR AlphaFoldDB; P09880; -.
DR SMR; P09880; -.
DR BioGRID; 33670; 20.
DR DIP; DIP-4611N; -.
DR IntAct; P09880; 4.
DR MINT; P09880; -.
DR STRING; 4932.YJL087C; -.
DR MaxQB; P09880; -.
DR PaxDb; P09880; -.
DR PRIDE; P09880; -.
DR EnsemblFungi; YJL087C_mRNA; YJL087C; YJL087C.
DR GeneID; 853358; -.
DR KEGG; sce:YJL087C; -.
DR SGD; S000003623; TRL1.
DR VEuPathDB; FungiDB:YJL087C; -.
DR eggNOG; ENOG502QQB9; Eukaryota.
DR HOGENOM; CLU_010316_1_0_1; -.
DR InParanoid; P09880; -.
DR OMA; YNQNHGI; -.
DR BioCyc; MetaCyc:G3O-31543-MON; -.
DR BioCyc; YEAST:G3O-31543-MON; -.
DR PRO; PR:P09880; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P09880; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005637; C:nuclear inner membrane; IDA:SGD.
DR GO; GO:0004113; F:2',3'-cyclic-nucleotide 3'-phosphodiesterase activity; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0051730; F:GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity; IDA:SGD.
DR GO; GO:0003972; F:RNA ligase (ATP) activity; IDA:SGD.
DR GO; GO:0036498; P:IRE1-mediated unfolded protein response; IMP:SGD.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0032056; P:positive regulation of translation in response to stress; IMP:SGD.
DR GO; GO:2000622; P:regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:SGD.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IDA:SGD.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR019039; RNA_ligase_T4-Rnl1_N.
DR InterPro; IPR012387; Trl1_fun.
DR InterPro; IPR015966; tRNA_lig_kin_fungi.
DR InterPro; IPR015965; tRNA_lig_PDEase.
DR Pfam; PF09511; RNA_lig_T4_1; 1.
DR Pfam; PF08302; tRNA_lig_CPD; 1.
DR Pfam; PF08303; tRNA_lig_kinase; 1.
DR PIRSF; PIRSF019634; tRNA_lig_yeast; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Endonuclease; Hydrolase; Kinase; Ligase;
KW Multifunctional enzyme; Nuclease; Nucleotide-binding; Reference proteome;
KW Transferase; tRNA processing.
FT CHAIN 1..827
FT /note="tRNA ligase"
FT /id="PRO_0000065635"
FT ACT_SITE 114
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000269|PubMed:2207062"
SQ SEQUENCE 827 AA; 95337 MW; 8D380B17891FE10A CRC64;
MPSPYDGKRT VTQLVNELEK AEKLSGRGRA YRRVCDLSHS NKKVISWKFN EWDYGKNTIT
LPCNARGLFI SDDTTNPVIV ARGYDKFFNV GEVNFTKWNW IEENCTGPYD VTIKANGCII
FISGLEDGTL VVCSKHSTGP RADVDRNHAE AGEKQLLRQL AAMNINRSDF ARMLYTHNVT
AVAEYCDDSF EEHILEYPLE KAGLYLHGVN VNKAEFETWD MKDVSQMASK YGFRCVQCIT
SNTLEDLKKF LDNCSATGSF EGQEIEGFVI RCHLKSTEKP FFFKYKFEEP YLMYRQWREV
TKDYISNKSR VFKFRKHKFI TNKYLDFAIP ILESSPKICE NYLKGFGVIE LRNKFLQSYG
MSGLEILNHE KVAELELKNA IDYDKVDERT KFLIFPISVI GCGKTTTSQT LVNLFPDSWG
HIQNDDITGK DKSQLMKKSL ELLSKKEIKC VIVDRNNHQF RERKQLFEWL NELKEDYLVY
DTNIKVIGVS FAPYDKLSEI RDITLQRVIK RGNNHQSIKW DELGEKKVVG IMNGFLKRYQ
PVNLDKSPDN MFDLMIELDF GQADSSLTNA KQILNEIHKA YPILVPEIPK DDEIETAFRR
SLDYKPTVRK IVGKGNNNQQ KTPKLIKPTY ISAKIENYDE IIELVKRCIA SDAELTEKFK
HLLASGKVQK ELHITLGHVM SSREKEAKKL WKSYCNRYTD QITEYNNNRI ENAQGSGNNQ
NTQVKTTDKL NFRLEKLCWD EKIIAIVVEL SKDKDGCIID ENNEKIKGLC CQNKIPHITL
CKLESGVKAV YSNVLCEKVE SAEVDENIKV VKLDNSKEFV GSVYLNF
