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Protein

Aspartate--tRNA(Asp) ligase

Gene

aspS

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of glutamate to tRNA(Asp) in a two-step reaction: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp).3 Publications

Catalytic activityi

ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).UniRule annotation2 Publications

Cofactori

Mg2+UniRule annotation1 PublicationNote: Binds 3 Mg2+ cations per subunit. The strongest magnesium site (Mg1) is bound to the beta- and gamma-phosphates of ATP and four water molecules complete its coordination sphere.UniRule annotation1 Publication

Kineticsi

kcat is 0.061 sec(-1) for tRNA(Asp) aspartylation (at 60 degrees Celsius).

  1. KM=1.4 µM for tRNA(Asp) (at 60 degrees Celsius)1 Publication

    Temperature dependencei

    Optimum temperature is 60 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei26Important for tRNA discrimination1
    Sitei85Important for tRNA discrimination1
    Binding sitei170Aspartate1
    Binding sitei214Aspartate1
    Metal bindingi361Magnesium 21
    Metal bindingi361Magnesium 31
    Binding sitei361ATP1
    Metal bindingi364Magnesium 21
    Binding sitei364Aspartate1
    Binding sitei368Aspartate1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi214 – 216ATP3
    Nucleotide bindingi222 – 224ATP3
    Nucleotide bindingi409 – 412ATP4

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi6.1.1.12. 5246.
    SABIO-RKQ52428.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Aspartate--tRNA(Asp) ligaseUniRule annotation (EC:6.1.1.12UniRule annotation)
    Alternative name(s):
    Aspartyl-tRNA synthetaseUniRule annotation
    Short name:
    AspRSUniRule annotation
    Discriminating aspartyl-tRNA synthetaseUniRule annotation
    Short name:
    D-AspRSUniRule annotation
    Gene namesi
    Name:aspSUniRule annotation
    Ordered Locus Names:TK0492
    OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    Proteomesi
    • UP000000536 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi26W → H: Gains the ability to form Asp-tRNA(Asn) in vitro. Only 2-fold decrease in catalytic efficiency for Asp-tRNA(Asp) synthesis. 1 Publication1
    Mutagenesisi85K → P: Gains the ability to form Asp-tRNA(Asn) in vitro, and is impaired in its ability to synthesize Asp-tRNA(Asp) due to a 8-fold decrease in affinity for tRNA(Asp). 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001110051 – 438Aspartate--tRNA(Asp) ligaseAdd BLAST438

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    STRINGi69014.TK0492.

    Structurei

    Secondary structure

    1438
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi7 – 9Combined sources3
    Helixi12 – 14Combined sources3
    Beta strandi18 – 31Combined sources14
    Beta strandi34 – 41Combined sources8
    Beta strandi44 – 51Combined sources8
    Turni52 – 54Combined sources3
    Helixi57 – 62Combined sources6
    Helixi63 – 65Combined sources3
    Beta strandi71 – 80Combined sources10
    Beta strandi87 – 99Combined sources13
    Beta strandi111 – 113Combined sources3
    Helixi117 – 122Combined sources6
    Helixi124 – 127Combined sources4
    Helixi131 – 153Combined sources23
    Beta strandi163 – 167Combined sources5
    Beta strandi172 – 174Combined sources3
    Beta strandi177 – 180Combined sources4
    Beta strandi183 – 187Combined sources5
    Helixi192 – 197Combined sources6
    Helixi198 – 200Combined sources3
    Beta strandi205 – 213Combined sources9
    Beta strandi225 – 236Combined sources12
    Helixi240 – 261Combined sources22
    Helixi263 – 268Combined sources6
    Beta strandi282 – 284Combined sources3
    Helixi285 – 294Combined sources10
    Helixi307 – 321Combined sources15
    Beta strandi324 – 330Combined sources7
    Helixi333 – 335Combined sources3
    Beta strandi344 – 346Combined sources3
    Beta strandi349 – 357Combined sources9
    Beta strandi360 – 368Combined sources9
    Helixi372 – 381Combined sources10
    Helixi386 – 389Combined sources4
    Helixi390 – 394Combined sources5
    Beta strandi403 – 409Combined sources7
    Helixi410 – 417Combined sources8
    Helixi423 – 426Combined sources4
    Beta strandi427 – 429Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B8AX-ray1.90A/B1-438[»]
    3NELX-ray1.95A/B1-438[»]
    3NEMX-ray1.89A/B1-438[»]
    3NENX-ray2.40A/B1-438[»]
    ProteinModelPortaliQ52428.
    SMRiQ52428.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ52428.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni192 – 195Aspartate4

    Sequence similaritiesi

    Belongs to the class-II aminoacyl-tRNA synthetase family. Type 2 subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiarCOG00406. Archaea.
    COG0017. LUCA.
    HOGENOMiHOG000226032.
    InParanoidiQ52428.
    KOiK01876.
    OMAiMENENAP.

    Family and domain databases

    HAMAPiMF_02075. Asp_tRNA_synth_type2. 1 hit.
    InterProiIPR004364. aa-tRNA-synt_II.
    IPR018150. aa-tRNA-synt_II-like.
    IPR006195. aa-tRNA-synth_II.
    IPR004523. Asp-tRNA_synthase_arc.
    IPR002312. Asp/Asn-tRNA-synth_IIb.
    IPR012340. NA-bd_OB-fold.
    IPR004365. NA-bd_OB_tRNA.
    [Graphical view]
    PANTHERiPTHR22594. PTHR22594. 1 hit.
    PTHR22594:SF10. PTHR22594:SF10. 1 hit.
    PfamiPF00152. tRNA-synt_2. 1 hit.
    PF01336. tRNA_anti-codon. 1 hit.
    [Graphical view]
    PRINTSiPR01042. TRNASYNTHASP.
    SUPFAMiSSF50249. SSF50249. 1 hit.
    TIGRFAMsiTIGR00458. aspS_nondisc. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q52428-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MYRTHYSSEI TEELNGQKVK VAGWVWEVKD LGGIKFLWIR DRDGIVQITA
    60 70 80 90 100
    PKKKVDPELF KLIPKLRSED VVAVEGVVNF TPKAKLGFEI LPEKIVVLNR
    110 120 130 140 150
    AETPLPLDPT GKVKAELDTR LDNRFMDLRR PEVMAIFKIR SSVFKAVRDF
    160 170 180 190 200
    FHENGFIEIH TPKIIATATE GGTELFPMKY FEEDAFLAQS PQLYKQIMMA
    210 220 230 240 250
    SGLDRVYEIA PIFRAEEHNT TRHLNEAWSI DSEMAFIEDE EEVMSFLERL
    260 270 280 290 300
    VAHAINYVRE HNAKELDILN FELEEPKLPF PRVSYDKALE ILGDLGKEIP
    310 320 330 340 350
    WGEDIDTEGE RLLGKYMMEN ENAPLYFLYQ YPSEAKPFYI MKYDNKPEIC
    360 370 380 390 400
    RAFDLEYRGV EISSGGQREH RHDILVEQIK EKGLNPESFE FYLKAFRYGM
    410 420 430
    PPHGGFGLGA ERLIKQMLDL PNIREVILFP RDRRRLTP
    Length:438
    Mass (Da):50,910
    Last modified:March 29, 2005 - v2
    Checksum:iE03C8766ADD2209A
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti413L → V in BAA08115 (PubMed:7590306).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D45167 Genomic DNA. Translation: BAA08115.1.
    AP006878 Genomic DNA. Translation: BAD84681.1.
    RefSeqiWP_011249447.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD84681; BAD84681; TK0492.
    GeneIDi3235903.
    KEGGitko:TK0492.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D45167 Genomic DNA. Translation: BAA08115.1.
    AP006878 Genomic DNA. Translation: BAD84681.1.
    RefSeqiWP_011249447.1. NC_006624.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B8AX-ray1.90A/B1-438[»]
    3NELX-ray1.95A/B1-438[»]
    3NEMX-ray1.89A/B1-438[»]
    3NENX-ray2.40A/B1-438[»]
    ProteinModelPortaliQ52428.
    SMRiQ52428.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi69014.TK0492.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD84681; BAD84681; TK0492.
    GeneIDi3235903.
    KEGGitko:TK0492.

    Phylogenomic databases

    eggNOGiarCOG00406. Archaea.
    COG0017. LUCA.
    HOGENOMiHOG000226032.
    InParanoidiQ52428.
    KOiK01876.
    OMAiMENENAP.

    Enzyme and pathway databases

    BRENDAi6.1.1.12. 5246.
    SABIO-RKQ52428.

    Miscellaneous databases

    EvolutionaryTraceiQ52428.

    Family and domain databases

    HAMAPiMF_02075. Asp_tRNA_synth_type2. 1 hit.
    InterProiIPR004364. aa-tRNA-synt_II.
    IPR018150. aa-tRNA-synt_II-like.
    IPR006195. aa-tRNA-synth_II.
    IPR004523. Asp-tRNA_synthase_arc.
    IPR002312. Asp/Asn-tRNA-synth_IIb.
    IPR012340. NA-bd_OB-fold.
    IPR004365. NA-bd_OB_tRNA.
    [Graphical view]
    PANTHERiPTHR22594. PTHR22594. 1 hit.
    PTHR22594:SF10. PTHR22594:SF10. 1 hit.
    PfamiPF00152. tRNA-synt_2. 1 hit.
    PF01336. tRNA_anti-codon. 1 hit.
    [Graphical view]
    PRINTSiPR01042. TRNASYNTHASP.
    SUPFAMiSSF50249. SSF50249. 1 hit.
    TIGRFAMsiTIGR00458. aspS_nondisc. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSYD_THEKO
    AccessioniPrimary (citable) accession number: Q52428
    Secondary accession number(s): Q5JD76
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: March 29, 2005
    Last modified: November 30, 2016
    This is version 128 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference 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

    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.