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Entry version 100 (08 May 2019)
Sequence version 2 (26 Jun 2007)
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Protein

Threonine--tRNA ligase editing subunit

Gene

thrS2

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Freestanding tRNA editing subunit of threonine--tRNA ligase, the catalytic subunit is probably AC Q9YDW0. Deacylates (edits) mischarged L-seryl-tRNA(Thr) in trans; has no activity on correctly charged L-threonyl-tRNA(Thr) (PubMed:26113036). Probably does not aminoacylate tRNA(Thr) (By similarity). Deacylates correctly charged glycyl-tRNA(Gly), but not glycyl-tRNA(Gly)(2'-dA76) (the terminal 2'-OH of tRNA adenine 76 has been dehydroxylated) nor the 2'-fluoro tRNA derivative, strongly suggesting the editing function is catalyzed by the 2'-OH of A76 of tRNA(Thr) (PubMed:26113036).By similarity1 Publication

Miscellaneous

There are two ThrRS in this archaeon. The first one (APE_0809.1, AC Q9YDW0) is most similar to bacterial ThrRS but it lacks the N-terminal editing domain. The second one (APE_0117.1, this entry) is most similar to archaeal ThrRS but lacks the central catalytic domain; it probably does not aminoacylate tRNA(Thr).Curated

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRNA-binding, tRNA-binding
Biological processProtein biosynthesis

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Threonine--tRNA ligase editing subunitCurated
Alternative name(s):
Ser-tRNA(Thr) hydrolaseCurated
Threonyl-tRNA synthetase 2
Short name:
ThrRS 21 Publication
Threonyl-tRNA synthetase editing subunitCurated
Short name:
ThrS-edCurated
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:thrS2
Ordered Locus Names:APE_0117.1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri272557 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002518 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi77H → A: Isolated domain has decreased deacylation of mischarged L-seryl-tRNA(Thr), no activity on L-threonyl-tRNA(Thr). Deacylates correctly charged glycyl-tRNA(Gly). 1 Publication1
Mutagenesisi115Y → A: Whole protein and isolated domain have nearly wild-type deacylation of mischarged L-seryl-tRNA(Thr), no activity on L-threonyl-tRNA(Thr). Same results; when associated with A-129. 1 Publication1
Mutagenesisi116K → M: Isolated domain does not deacylate mischarged L-seryl-tRNA(Thr), no activity on L-threonyl-tRNA(Thr). 1 Publication1
Mutagenesisi129E → A: Whole protein and isolated domain have nearly wild-type deacylation of mischarged L-seryl-tRNA(Thr), no activity on L-threonyl-tRNA(Thr). Same results; when associated with A-115. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001011181 – 421Threonine--tRNA ligase editing subunitAdd BLAST421

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q9YFY3

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Probably interacts with its catalytic subunit (By similarity).By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
272557.APE_0117.1

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1421
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4RR6X-ray1.88A1-136[»]
4RR7X-ray1.86A1-136[»]
4RR8X-ray1.86A1-136[»]
4RR9X-ray1.67A1-136[»]
4RRAX-ray1.70A1-136[»]
4RRBX-ray2.10A1-136[»]
4RRCX-ray1.86A1-136[»]
4RRDX-ray1.86A1-136[»]
4RRHX-ray1.55A1-136[»]
4RRIX-ray1.50A1-136[»]
4RRJX-ray1.86A1-136[»]
4RRKX-ray1.86A1-136[»]
4RRLX-ray1.97A1-136[»]
4RRMX-ray1.55A1-136[»]

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q9YFY3

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The N-terminal domain (about residues 1-140) is an archaea-specific tRNA-editing domain (PubMed:26113036) that has a highly similar structure to Dtd (D-aminoacyl-tRNA deacylase). Editing of incorrectly charged L-seryl-tRNA(Thr) by this domain is tRNA catalyzed (PubMed:26113036).1 Publication

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
arCOG00401 Archaea
COG0441 LUCA

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.800, 1 hit
3.50.80.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR004154 Anticodon-bd
IPR036621 Anticodon-bd_dom_sf
IPR023509 DTD-like_sf
IPR002320 Thr-tRNA-ligase_IIa
IPR015011 Threonyl-tRNA_syn_edit_dom_arc

The PANTHER Classification System

More...
PANTHERi
PTHR11451 PTHR11451, 2 hits

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03129 HGTP_anticodon, 1 hit
PF08915 tRNA-Thr_ED, 1 hit

ProDom; a protein domain database

More...
ProDomi
View protein in ProDom or Entries sharing at least one domain
PD016189 tRNA-Thr_ED_arc, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q9YFY3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRLLYLHADR FEYKTVKPAL KNPPDPPGEA SFGEALVVFT TVEDGDGPQT
60 70 80 90 100
VMYAASDIAS HSSRLKVTTV ILYPYAHLSS RLAKPMAAHK RLIELEGALR
110 120 130 140 150
TKFPGHVHRA PFGWYKSFSI ACKGHPLAEL SRSFTEAGAL QPWPAVEDYK
160 170 180 190 200
TGLSGEVLAR AGLLGGGSLS PASWALEVHR RLAEEVVGPA ESVGFGESLS
210 220 230 240 250
EAYQACISSS VTTLLMGPYP PSIVFGPLED DPVEAVSRVL GLISPQLEGV
260 270 280 290 300
KPLLSGGEGA LKASSPDGAE LPVAFLKEGR VCLGPTLSFF KLAVSMLVEK
310 320 330 340 350
ARKEGLTPYL NPTLTPVQSA VIPVDSESEG YAQRIAEDLA ASGVRVSIVR
360 370 380 390 400
GSGLGRRVRE AGRSWASLVI VVGKREEETG TVVVRRRWEP GKQEVLTLDE
410 420
LSSEAKKLAS GSRGSLYSTT L
Length:421
Mass (Da):45,003
Last modified:June 26, 2007 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i9B311637CE9FBC73
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
BA000002 Genomic DNA Translation: BAA79028.2

Protein sequence database of the Protein Information Resource

More...
PIRi
B72766

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
BAA79028; BAA79028; APE_0117.1

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ape:APE_0117.1

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA Translation: BAA79028.2
PIRiB72766

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4RR6X-ray1.88A1-136[»]
4RR7X-ray1.86A1-136[»]
4RR8X-ray1.86A1-136[»]
4RR9X-ray1.67A1-136[»]
4RRAX-ray1.70A1-136[»]
4RRBX-ray2.10A1-136[»]
4RRCX-ray1.86A1-136[»]
4RRDX-ray1.86A1-136[»]
4RRHX-ray1.55A1-136[»]
4RRIX-ray1.50A1-136[»]
4RRJX-ray1.86A1-136[»]
4RRKX-ray1.86A1-136[»]
4RRLX-ray1.97A1-136[»]
4RRMX-ray1.55A1-136[»]
SMRiQ9YFY3
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272557.APE_0117.1

Proteomic databases

PRIDEiQ9YFY3

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA79028; BAA79028; APE_0117.1
KEGGiape:APE_0117.1

Phylogenomic databases

eggNOGiarCOG00401 Archaea
COG0441 LUCA

Family and domain databases

Gene3Di3.40.50.800, 1 hit
3.50.80.10, 1 hit
InterProiView protein in InterPro
IPR004154 Anticodon-bd
IPR036621 Anticodon-bd_dom_sf
IPR023509 DTD-like_sf
IPR002320 Thr-tRNA-ligase_IIa
IPR015011 Threonyl-tRNA_syn_edit_dom_arc
PANTHERiPTHR11451 PTHR11451, 2 hits
PfamiView protein in Pfam
PF03129 HGTP_anticodon, 1 hit
PF08915 tRNA-Thr_ED, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD016189 tRNA-Thr_ED_arc, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiSYTE_AERPE
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9YFY3
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: June 26, 2007
Last modified: May 8, 2019
This is version 100 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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