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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).UniRule annotation3 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)LengthDescriptionGraphical viewFeature identifierActions
    Sitei26 – 261Important for tRNA discrimination
    Sitei85 – 851Important for tRNA discrimination
    Binding sitei170 – 1701Aspartate
    Binding sitei214 – 2141Aspartate
    Metal bindingi361 – 3611Magnesium 2
    Metal bindingi361 – 3611Magnesium 3
    Binding sitei361 – 3611ATP
    Metal bindingi364 – 3641Magnesium 2
    Binding sitei364 – 3641Aspartate
    Binding sitei368 – 3681Aspartate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi214 – 2163ATP
    Nucleotide bindingi222 – 2243ATP
    Nucleotide bindingi409 – 4124ATP

    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

    BioCyciTKOD69014:GH72-500-MONOMER.
    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

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi26 – 261W → H: Gains the ability to form Asp-tRNA(Asn) in vitro. Only 2-fold decrease in catalytic efficiency for Asp-tRNA(Asp) synthesis. 1 Publication
    Mutagenesisi85 – 851K → 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 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 438438Aspartate--tRNA(Asp) ligasePRO_0000111005Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    STRINGi69014.TK0492.

    Structurei

    Secondary structure

    1
    438
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi7 – 93Combined sources
    Helixi12 – 143Combined sources
    Beta strandi18 – 3114Combined sources
    Beta strandi34 – 418Combined sources
    Beta strandi44 – 518Combined sources
    Turni52 – 543Combined sources
    Helixi57 – 626Combined sources
    Helixi63 – 653Combined sources
    Beta strandi71 – 8010Combined sources
    Beta strandi87 – 9913Combined sources
    Beta strandi111 – 1133Combined sources
    Helixi117 – 1226Combined sources
    Helixi124 – 1274Combined sources
    Helixi131 – 15323Combined sources
    Beta strandi163 – 1675Combined sources
    Beta strandi172 – 1743Combined sources
    Beta strandi177 – 1804Combined sources
    Beta strandi183 – 1875Combined sources
    Helixi192 – 1976Combined sources
    Helixi198 – 2003Combined sources
    Beta strandi205 – 2139Combined sources
    Beta strandi225 – 23612Combined sources
    Helixi240 – 26122Combined sources
    Helixi263 – 2686Combined sources
    Beta strandi282 – 2843Combined sources
    Helixi285 – 29410Combined sources
    Helixi307 – 32115Combined sources
    Beta strandi324 – 3307Combined sources
    Helixi333 – 3353Combined sources
    Beta strandi344 – 3463Combined sources
    Beta strandi349 – 3579Combined sources
    Beta strandi360 – 3689Combined sources
    Helixi372 – 38110Combined sources
    Helixi386 – 3894Combined sources
    Helixi390 – 3945Combined sources
    Beta strandi403 – 4097Combined sources
    Helixi410 – 4178Combined sources
    Helixi423 – 4264Combined sources
    Beta strandi427 – 4293Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-438.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ52428.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni192 – 1954Aspartate

    Sequence similaritiesi

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

    Phylogenomic databases

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

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    HAMAPiMF_00044. Asp_tRNA_synth.
    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti413 – 4131L → V in BAA08115 (PubMed:7590306).Curated

    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
    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. Positions 1-438.
    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.
    OMAiKPEICRA.

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-500-MONOMER.
    BRENDAi6.1.1.12. 5246.
    SABIO-RKQ52428.

    Miscellaneous databases

    EvolutionaryTraceiQ52428.

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    HAMAPiMF_00044. Asp_tRNA_synth.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Aspartyl-tRNA synthetase of the hyperthermophilic archaeon Pyrococcus sp. KOD1 has a chimerical structure of eukaryotic and bacterial enzymes."
      Imanaka T., Lee S., Takagi M., Fujiwara S.
      Gene 164:153-156(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    2. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
      Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
      Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    3. "Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms."
      Tumbula-Hansen D., Feng L., Toogood H., Stetter K.O., Soll D.
      J. Biol. Chem. 277:37184-37190(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A DISCRIMINATING ASPRS.
    4. "Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain."
      Charron C., Roy H., Blaise M., Giege R., Kern D.
      EMBO J. 22:1632-1643(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A DISCRIMINATING ASPRS, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    5. "Expanding tRNA recognition of a tRNA synthetase by a single amino acid change."
      Feng L., Tumbula-Hansen D., Toogood H., Soll D.
      Proc. Natl. Acad. Sci. U.S.A. 100:5676-5681(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A DISCRIMINATING ASPRS, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF TRP-26 AND LYS-85, DISCRIMINATION SITES.
    6. "Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation."
      Schmitt E., Moulinier L., Fujiwara S., Imanaka T., Thierry J.-C., Moras D.
      EMBO J. 17:5227-5237(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH ATP-MG; ASPARTATE AND ASPARTYL-AMP, COFACTOR, SUBUNIT.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.

    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 11, 2015
    This is version 124 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.