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Protein

Threonine--tRNA ligase

Gene

thrS

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr) (Probable). Edits incorrectly charged L-seryl-tRNA(Thr) via its editing domain (PubMed:16902403, PubMed:21098258). Deacylates correctly charged glycyl-tRNA(Gly), but neither glycyl-tRNA(Gly)(2'-dA76) (the terminal 2'-OH of tRNA(Thr) adenine 76 has been replaced by hydrogen) nor the 2'-fluoro tRNA derivative do so, strongly suggesting the editing function is tRNA catalyzed (PubMed:26113036).3 Publications

Catalytic activityi

ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).UniRule annotation

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi298ZincUniRule annotation1
Metal bindingi350Zinc; via tele nitrogenUniRule annotation1
Metal bindingi474Zinc; via pros nitrogenUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAminoacyl-tRNA synthetase, Ligase, RNA-binding, tRNA-binding
Biological processProtein biosynthesis
LigandATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BRENDAi6.1.1.3. 5242.

Names & Taxonomyi

Protein namesi
Recommended name:
Threonine--tRNA ligaseUniRule annotation (EC:6.1.1.3UniRule annotation)
Alternative name(s):
Threonyl-tRNA synthetaseUniRule annotation
Short name:
ThrRSUniRule annotation
Gene namesi
Name:thrSUniRule annotation
Ordered Locus Names:PYRAB13430
ORF Names:PAB1490
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000810 Componenti: Chromosome
  • UP000009139 Componenti: Chromosome

Subcellular locationi

Q9UZ14:
  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi83H → A: Isolated domain has decreased to no deacylation of mischarged L-seryl-tRNA(Thr). Deacylates correctly charged glycyl-tRNA(Gly). 2 Publications1
Mutagenesisi120Y → A: Isolated domain has nearly wild-type deacylation of mischarged L-seryl-tRNA(Thr), no longer binds L-Ser or L-Cys. No activity on threonyl-tRNA(Thr). Same results; when associated with A-134. 2 Publications1
Mutagenesisi121K → M: Isolated domain has nearly wild-type deacylation of mischarged L-seryl-tRNA(Thr). Later shown not to deacylate L-seryl-tRNA(Thr), no activity on L-threonyl-tRNA(Thr). 2 Publications1
Mutagenesisi121K → S: Isolated domain does not deacylate mischarged L-seryl-tRNA(Thr). 1 Publication1
Mutagenesisi134E → A: Isolated domain has nearly wild-type deacylation of mischarged L-seryl-tRNA(Thr). No activity on L-threonyl-tRNA(Thr). Same results; when associated with A-120. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001011071 – 625Threonine--tRNA ligaseAdd BLAST625

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi272844.PAB1490.

Structurei

Secondary structure

1625
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 22Combined sources21
Helixi28 – 31Combined sources4
Beta strandi32 – 44Combined sources13
Helixi47 – 51Combined sources5
Helixi53 – 71Combined sources19
Beta strandi75 – 80Combined sources6
Helixi82 – 84Combined sources3
Beta strandi86 – 88Combined sources3
Helixi91 – 107Combined sources17
Beta strandi111 – 114Combined sources4
Beta strandi117 – 127Combined sources11
Beta strandi133 – 138Combined sources6
Helixi142 – 144Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Y2QX-ray1.95A1-143[»]
2HKZX-ray2.10A1-143[»]
2HL0X-ray1.86A1-143[»]
2HL1X-ray2.25A/B1-147[»]
2HL2X-ray2.60A/B1-143[»]
3PD2X-ray1.86A/B1-147[»]
3PD3X-ray1.86A/B1-147[»]
3PD4X-ray2.40A/B1-147[»]
3PD5X-ray2.29A/B1-147[»]
4RRQX-ray1.79A/B1-147[»]
4RRRX-ray1.86A/B1-147[»]
4S02X-ray1.95A1-143[»]
4S03X-ray2.05A1-143[»]
4S0IX-ray2.36A1-143[»]
4S0JX-ray2.10A1-143[»]
4S0KX-ray2.10A1-143[»]
4S0LX-ray2.50A1-143[»]
ProteinModelPortaliQ9UZ14.
SMRiQ9UZ14.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UZ14.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 143Editing domainUniRule annotation4 PublicationsAdd BLAST143
Regioni206 – 505CatalyticUniRule annotationAdd BLAST300

Domaini

The N-terminal domain (about residues 1-143) is an archaea-specific tRNA-editing domain (PubMed:16902403) that has a highly similar structure to Dtd (D-aminoacyl-tRNA deacylase); the domain binds L-serine and L-cysteine and most D-amino acids but not L-threonine (PubMed:15908961, PubMed:16902403). Editing of incorrectly charged L-seryl-tRNA(Thr) by this domain is tRNA catalyzed (PubMed:16902403, PubMed:21098258, PubMed:26113036).4 Publications

Sequence similaritiesi

Belongs to the class-II aminoacyl-tRNA synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG00401. Archaea.
COG0441. LUCA.
HOGENOMiHOG000073571.
KOiK01868.
OMAiDAHIFML.
OrthoDBiPOG093Z01GO.

Family and domain databases

CDDicd00771. ThrRS_core. 1 hit.
Gene3Di3.40.50.800. 1 hit.
HAMAPiMF_00184. Thr_tRNA_synth. 1 hit.
InterProiView protein in InterPro
IPR002314. aa-tRNA-synt_IIb.
IPR006195. aa-tRNA-synth_II.
IPR004154. Anticodon-bd.
IPR036621. Anticodon-bd_dom_sf.
IPR002320. Thr-tRNA-ligase_IIa.
IPR015011. Threonyl-tRNA_syn_edit_dom_arc.
IPR033728. ThrRS_core.
PANTHERiPTHR11451. PTHR11451. 1 hit.
PfamiView protein in Pfam
PF03129. HGTP_anticodon. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
PF08915. tRNA-Thr_ED. 1 hit.
PRINTSiPR01047. TRNASYNTHTHR.
ProDomiView protein in ProDom or Entries sharing at least one domain
PD016189. tRNA-Thr_ED_arc. 1 hit.
SUPFAMiSSF52954. SSF52954. 1 hit.
TIGRFAMsiTIGR00418. thrS. 1 hit.
PROSITEiView protein in PROSITE
PS50862. AA_TRNA_LIGASE_II. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9UZ14-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVLLIHSDY IEYEVKDKAL KNPEPISEDM KRGRMEEVLV AFISVEKVDE
60 70 80 90 100
KNPEEVSLKA IEEISKVAEQ VKAENVFVYP FAHLSSELAK PSVAMDILNR
110 120 130 140 150
VYQGLKERGF NVGKAPFGYY KAFKISCKGH PLAELSRTIV PEEARVEEVP
160 170 180 190 200
EALRKEEEEL VSYWYILTPE GELIEVDKFD FTGYENLRKF VNYEIAKNRI
210 220 230 240 250
AEKEPPHVKL MLEHELVDYE PGSDPGNLRY YPKGRLIKSL LEQYVTEKVI
260 270 280 290 300
EYGAMEVETP IMYDFEHPAL EKYLNRFPAR QYIVLSGDKR YFLRFAACFG
310 320 330 340 350
QFMIKKDAII SYRNLPLRMY ELTRYSFRRE KRGELSGLRR LRAFTMPDMH
360 370 380 390 400
TLAKDIEQAK EEFKKQFKLS MEVLEGVGLT PEDYEVAIRF TEDFWKEHKD
410 420 430 440 450
FIVELVKLIG KPVLIEMWKQ RFFYFILKFE FNFVDNLDKA AALSTVQIDV
460 470 480 490 500
ENAERFGITY YDENGEEKYP LILHCSPSGA IERVMYAILE KQAKLMNEGK
510 520 530 540 550
KPMFPLWLSP IQVRVIPVSE EYLDYALYVA GKLEGAKIRV DVDDEDERLN
560 570 580 590 600
KKIRRAEKEW IPYIVVVGAR EKENGTITVR RREDGKQYET RIEELIKEIK
610 620
EKTEGFPYKP RPLPLLLSKR PKFRG
Length:625
Mass (Da):73,372
Last modified:May 1, 2000 - v1
Checksum:iAF8E48AAE789124F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248287 Genomic DNA. Translation: CAB50248.1.
HE613800 Genomic DNA. Translation: CCE70785.1.
PIRiC75044.
RefSeqiWP_010868458.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB50248; CAB50248; PAB1490.
GeneIDi1496731.
KEGGipab:PAB1490.
PATRICifig|272844.11.peg.1427.

Similar proteinsi

Entry informationi

Entry nameiSYT_PYRAB
AccessioniPrimary (citable) accession number: Q9UZ14
Secondary accession number(s): G8ZHE8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: May 1, 2000
Last modified: October 25, 2017
This is version 125 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families