Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

tRNA ligase

Gene

TRL1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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.

Catalytic activityi

ATP + (ribonucleotide)(n) + (ribonucleotide)(m) = AMP + diphosphate + (ribonucleotide)(n+m).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei114 – 1141N6-AMP-lysine intermediate1 Publication

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
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Kinase, Ligase, Nuclease, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16152.
YEAST:G3O-31543-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA ligase (EC:6.5.1.3)
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

GO - Cellular componenti

  • nuclear inner membrane Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 827827tRNA ligasePRO_0000065635Add
BLAST

Proteomic databases

MaxQBiP09880.
PeptideAtlasiP09880.

Interactioni

Protein-protein interaction databases

BioGridi33670. 14 interactions.
DIPiDIP-4611N.
MINTiMINT-527662.

Structurei

3D structure databases

ProteinModelPortaliP09880.
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.
OMAiQDWFFKY.
OrthoDBiEOG7XH6ZF.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR019039. RNA_ligase_T4-Rnl1_N.
IPR012387. Trl1_fun.
IPR015966. tRNA_lig_kin_fun.
IPR015965. tRNA_lig_PDEase_fun.
[Graphical view]
PfamiPF09511. RNA_lig_T4_1. 1 hit.
PF08302. tRNA_lig_CPD. 1 hit.
PF08303. tRNA_lig_kinase. 1 hit.
[Graphical view]
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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP09880.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33670. 14 interactions.
DIPiDIP-4611N.
MINTiMINT-527662.

Proteomic databases

MaxQBiP09880.
PeptideAtlasiP09880.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJL087C; YJL087C; YJL087C.
GeneIDi853358.
KEGGisce:YJL087C.

Organism-specific databases

EuPathDBiFungiDB:YJL087C.
SGDiS000003623. TRL1.

Phylogenomic databases

HOGENOMiHOG000208273.
InParanoidiP09880.
KOiK14679.
OMAiQDWFFKY.
OrthoDBiEOG7XH6ZF.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16152.
YEAST:G3O-31543-MONOMER.

Miscellaneous databases

NextBioi973777.
PROiP09880.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR019039. RNA_ligase_T4-Rnl1_N.
IPR012387. Trl1_fun.
IPR015966. tRNA_lig_kin_fun.
IPR015965. tRNA_lig_PDEase_fun.
[Graphical view]
PfamiPF09511. RNA_lig_T4_1. 1 hit.
PF08302. tRNA_lig_CPD. 1 hit.
PF08303. tRNA_lig_kinase. 1 hit.
[Graphical view]
PIRSFiPIRSF019634. tRNA_lig_yeast. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure and function of the yeast tRNA ligase gene."
    Westaway S.K., Phizicky E.M., Abelson J.
    J. Biol. Chem. 263:3171-3176(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequence analysis of a 33.1 kb fragment from the left arm of Saccharomyces cerevisiae chromosome X, including putative proteins with leucine zippers, a fungal Zn(II)2-Cys6 binuclear cluster domain and a putative alpha 2-SCB-alpha 2 binding site."
    Miosga T., Schaaff-Gerstenschlaeger I., Chalwatzis N., Baur A., Boles E., Fournier C., Schmitt S., Velten C., Wilhelm N., Zimmermann F.K.
    Yeast 11:681-689(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: ACTIVE SITE.
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiTRNL_YEAST
AccessioniPrimary (citable) accession number: P09880
Secondary accession number(s): D6VW97
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: May 11, 2016
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.