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Protein

tRNA ligase

Gene

TRL1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

One of the two proteins required for the splicing of precursor tRNA molecules containing introns. The ligation activity requires three enzymatic activities: phosphorylation of the 5' terminus of the 3' half-tRNA in the presence of ATP, opening of the 2'3'-cyclic phosphodiester bond of the 5' half-tRNA leaving a 2'-phosphomonoester and ligation of the two tRNA halves in an ATP-dependent reaction.

Miscellaneous

tRNA ligase is a relatively rare protein with about 400 copies per yeast cell.
Present with 3110 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

ATP + (ribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(ribonucleotide)(m) = (ribonucleotide)(n+m) + AMP + diphosphate.Curated

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei114N6-AMP-lysine intermediate1 Publication1

GO - Molecular functioni

  • 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity Source: SGD
  • ATP binding Source: UniProtKB-KW
  • endonuclease activity Source: UniProtKB-KW
  • GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity Source: SGD
  • RNA ligase (ATP) activity Source: SGD

GO - Biological processi

  • mRNA splicing via endonucleolytic cleavage and ligation involved in unfolded protein response Source: SGD
  • positive regulation of translation in response to stress Source: SGD
  • tRNA splicing, via endonucleolytic cleavage and ligation Source: SGD

Keywordsi

Molecular functionEndonuclease, Hydrolase, Kinase, Ligase, Multifunctional enzyme, Nuclease, Transferase
Biological processtRNA processing
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:G3O-31543-MONOMER
YEAST:G3O-31543-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA ligase (EC:6.5.1.3Curated)
Gene namesi
Name:TRL1
Synonyms:RLG1
Ordered Locus Names:YJL087C
ORF Names:J0927
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJL087C
SGDiS000003623 TRL1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000656351 – 827tRNA ligaseAdd BLAST827

Proteomic databases

MaxQBiP09880
PaxDbiP09880
PRIDEiP09880

Interactioni

Protein-protein interaction databases

BioGridi33670, 17 interactors
DIPiDIP-4611N
IntActiP09880, 17 interactors
MINTiP09880
STRINGi4932.YJL087C

Structurei

3D structure databases

ProteinModelPortaliP09880
SMRiP09880
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Has three domains each corresponding to an enzymatic activity, namely in N- to C-terminal order: ligase, kinase and cyclic phosphodiesterase (CPDase).

Sequence similaritiesi

Belongs to the TRL1 family.Curated

Phylogenomic databases

HOGENOMiHOG000208273
InParanoidiP09880
KOiK14679
OMAiVKPKESN
OrthoDBiEOG092C1J71

Family and domain databases

InterProiView protein in InterPro
IPR027417 P-loop_NTPase
IPR019039 RNA_ligase_T4-Rnl1_N
IPR012387 Trl1_fun
IPR015966 tRNA_lig_kin_fungi
IPR015965 tRNA_lig_PDEase
PfamiView protein in Pfam
PF09511 RNA_lig_T4_1, 1 hit
PF08302 tRNA_lig_CPD, 1 hit
PF08303 tRNA_lig_kinase, 1 hit
PIRSFiPIRSF019634 tRNA_lig_yeast, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit

Sequencei

Sequence statusi: Complete.

P09880-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPSPYDGKRT VTQLVNELEK AEKLSGRGRA YRRVCDLSHS NKKVISWKFN
60 70 80 90 100
EWDYGKNTIT LPCNARGLFI SDDTTNPVIV ARGYDKFFNV GEVNFTKWNW
110 120 130 140 150
IEENCTGPYD VTIKANGCII FISGLEDGTL VVCSKHSTGP RADVDRNHAE
160 170 180 190 200
AGEKQLLRQL AAMNINRSDF ARMLYTHNVT AVAEYCDDSF EEHILEYPLE
210 220 230 240 250
KAGLYLHGVN VNKAEFETWD MKDVSQMASK YGFRCVQCIT SNTLEDLKKF
260 270 280 290 300
LDNCSATGSF EGQEIEGFVI RCHLKSTEKP FFFKYKFEEP YLMYRQWREV
310 320 330 340 350
TKDYISNKSR VFKFRKHKFI TNKYLDFAIP ILESSPKICE NYLKGFGVIE
360 370 380 390 400
LRNKFLQSYG MSGLEILNHE KVAELELKNA IDYDKVDERT KFLIFPISVI
410 420 430 440 450
GCGKTTTSQT LVNLFPDSWG HIQNDDITGK DKSQLMKKSL ELLSKKEIKC
460 470 480 490 500
VIVDRNNHQF RERKQLFEWL NELKEDYLVY DTNIKVIGVS FAPYDKLSEI
510 520 530 540 550
RDITLQRVIK RGNNHQSIKW DELGEKKVVG IMNGFLKRYQ PVNLDKSPDN
560 570 580 590 600
MFDLMIELDF GQADSSLTNA KQILNEIHKA YPILVPEIPK DDEIETAFRR
610 620 630 640 650
SLDYKPTVRK IVGKGNNNQQ KTPKLIKPTY ISAKIENYDE IIELVKRCIA
660 670 680 690 700
SDAELTEKFK HLLASGKVQK ELHITLGHVM SSREKEAKKL WKSYCNRYTD
710 720 730 740 750
QITEYNNNRI ENAQGSGNNQ NTQVKTTDKL NFRLEKLCWD EKIIAIVVEL
760 770 780 790 800
SKDKDGCIID ENNEKIKGLC CQNKIPHITL CKLESGVKAV YSNVLCEKVE
810 820
SAEVDENIKV VKLDNSKEFV GSVYLNF
Length:827
Mass (Da):95,337
Last modified:July 1, 1989 - v1
Checksum:i8D380B17891FE10A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03546 Genomic DNA Translation: AAA66921.1
X83502 Genomic DNA Translation: CAA58482.1
Z49362 Genomic DNA Translation: CAA89378.1
BK006943 Genomic DNA Translation: DAA08713.1
PIRiA29917
RefSeqiNP_012448.1, NM_001181520.1

Genome annotation databases

EnsemblFungiiYJL087C; YJL087C; YJL087C
GeneIDi853358
KEGGisce:YJL087C

Similar proteinsi

Entry informationi

Entry nameiTRNL_YEAST
AccessioniPrimary (citable) accession number: P09880
Secondary accession number(s): D6VW97
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: March 28, 2018
This is version 145 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health