ID SYD_THEKO Reviewed; 438 AA.
AC Q52428; Q5JD76;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 29-MAR-2005, sequence version 2.
DT 27-MAR-2024, entry version 158.
DE RecName: Full=Aspartate--tRNA(Asp) ligase {ECO:0000255|HAMAP-Rule:MF_02075};
DE EC=6.1.1.12 {ECO:0000255|HAMAP-Rule:MF_02075};
DE AltName: Full=Aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_02075};
DE Short=AspRS {ECO:0000255|HAMAP-Rule:MF_02075};
DE AltName: Full=Discriminating aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_02075};
DE Short=D-AspRS {ECO:0000255|HAMAP-Rule:MF_02075};
GN Name=aspS {ECO:0000255|HAMAP-Rule:MF_02075}; OrderedLocusNames=TK0492;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=7590306; DOI=10.1016/0378-1119(95)00491-n;
RA Imanaka T., Lee S., Takagi M., Fujiwara S.;
RT "Aspartyl-tRNA synthetase of the hyperthermophilic archaeon Pyrococcus sp.
RT KOD1 has a chimerical structure of eukaryotic and bacterial enzymes.";
RL Gene 164:153-156(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [3]
RP FUNCTION AS A DISCRIMINATING ASPRS.
RX PubMed=12149259; DOI=10.1074/jbc.m204767200;
RA Tumbula-Hansen D., Feng L., Toogood H., Stetter K.O., Soll D.;
RT "Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into
RT discriminating and nondiscriminating forms.";
RL J. Biol. Chem. 277:37184-37190(2002).
RN [4]
RP FUNCTION AS A DISCRIMINATING ASPRS, CATALYTIC ACTIVITY, AND SUBSTRATE
RP SPECIFICITY.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=12660169; DOI=10.1093/emboj/cdg148;
RA Charron C., Roy H., Blaise M., Giege R., Kern D.;
RT "Non-discriminating and discriminating aspartyl-tRNA synthetases differ in
RT the anticodon-binding domain.";
RL EMBO J. 22:1632-1643(2003).
RN [5]
RP FUNCTION AS A DISCRIMINATING ASPRS, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF TRP-26 AND
RP LYS-85, AND DISCRIMINATION SITES.
RX PubMed=12730374; DOI=10.1073/pnas.0631525100;
RA Feng L., Tumbula-Hansen D., Toogood H., Soll D.;
RT "Expanding tRNA recognition of a tRNA synthetase by a single amino acid
RT change.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:5676-5681(2003).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP ATP-MG; ASPARTATE AND ASPARTYL-AMP, COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=9724658; DOI=10.1093/emboj/17.17.5227;
RA Schmitt E., Moulinier L., Fujiwara S., Imanaka T., Thierry J.-C., Moras D.;
RT "Crystal structure of aspartyl-tRNA synthetase from Pyrococcus
RT kodakaraensis KOD: archaeon specificity and catalytic mechanism of
RT adenylate formation.";
RL EMBO J. 17:5227-5237(1998).
CC -!- FUNCTION: Catalyzes the attachment of L-aspartate to tRNA(Asp) in a
CC two-step reaction: L-aspartate is first activated by ATP to form Asp-
CC AMP and then transferred to the acceptor end of tRNA(Asp). Is specific
CC for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude
CC less efficiently than tRNA(Asp). {ECO:0000269|PubMed:12149259,
CC ECO:0000269|PubMed:12660169, ECO:0000269|PubMed:12730374}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-
CC aspartyl-tRNA(Asp); Xref=Rhea:RHEA:19649, Rhea:RHEA-COMP:9660,
CC Rhea:RHEA-COMP:9678, ChEBI:CHEBI:29991, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:78442, ChEBI:CHEBI:78516,
CC ChEBI:CHEBI:456215; EC=6.1.1.12; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_02075, ECO:0000269|PubMed:12660169,
CC ECO:0000269|PubMed:12730374};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02075,
CC ECO:0000269|PubMed:9724658};
CC Note=Binds 3 Mg(2+) cations per subunit. The strongest magnesium site
CC (Mg1) is bound to the beta- and gamma-phosphates of ATP and four water
CC molecules complete its coordination sphere. {ECO:0000255|HAMAP-
CC Rule:MF_02075, ECO:0000269|PubMed:9724658};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.4 uM for tRNA(Asp) (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12730374};
CC Note=kcat is 0.061 sec(-1) for tRNA(Asp) aspartylation (at 60 degrees
CC Celsius).;
CC Temperature dependence:
CC Optimum temperature is 60 degrees Celsius.
CC {ECO:0000269|PubMed:12730374};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_02075,
CC ECO:0000269|PubMed:9724658}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_02075}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type 2 subfamily. {ECO:0000255|HAMAP-Rule:MF_02075}.
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DR EMBL; D45167; BAA08115.1; -; Genomic_DNA.
DR EMBL; AP006878; BAD84681.1; -; Genomic_DNA.
DR RefSeq; WP_011249447.1; NC_006624.1.
DR PDB; 1B8A; X-ray; 1.90 A; A/B=1-438.
DR PDB; 3NEL; X-ray; 1.95 A; A/B=1-438.
DR PDB; 3NEM; X-ray; 1.89 A; A/B=1-438.
DR PDB; 3NEN; X-ray; 2.40 A; A/B=1-438.
DR PDBsum; 1B8A; -.
DR PDBsum; 3NEL; -.
DR PDBsum; 3NEM; -.
DR PDBsum; 3NEN; -.
DR AlphaFoldDB; Q52428; -.
DR SMR; Q52428; -.
DR STRING; 69014.TK0492; -.
DR EnsemblBacteria; BAD84681; BAD84681; TK0492.
DR GeneID; 78447003; -.
DR KEGG; tko:TK0492; -.
DR PATRIC; fig|69014.16.peg.483; -.
DR eggNOG; arCOG00406; Archaea.
DR HOGENOM; CLU_004553_2_1_2; -.
DR InParanoid; Q52428; -.
DR OrthoDB; 5908at2157; -.
DR PhylomeDB; Q52428; -.
DR BRENDA; 6.1.1.12; 5246.
DR SABIO-RK; Q52428; -.
DR EvolutionaryTrace; Q52428; -.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0017101; C:aminoacyl-tRNA synthetase multienzyme complex; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004815; F:aspartate-tRNA ligase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0006422; P:aspartyl-tRNA aminoacylation; IBA:GO_Central.
DR CDD; cd00776; AsxRS_core; 1.
DR CDD; cd04316; ND_PkAspRS_like_N; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR HAMAP; MF_02075; Asp_tRNA_synth_type2; 1.
DR InterPro; IPR004364; Aa-tRNA-synt_II.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR004523; Asp-tRNA_synthase_2.
DR InterPro; IPR002312; Asp/Asn-tRNA-synth_IIb.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004365; NA-bd_OB_tRNA.
DR NCBIfam; TIGR00458; aspS_nondisc; 1.
DR PANTHER; PTHR43450:SF1; ASPARTATE--TRNA LIGASE, CYTOPLASMIC; 1.
DR PANTHER; PTHR43450; ASPARTYL-TRNA SYNTHETASE; 1.
DR Pfam; PF00152; tRNA-synt_2; 1.
DR Pfam; PF01336; tRNA_anti-codon; 1.
DR PRINTS; PR01042; TRNASYNTHASP.
DR SUPFAM; SSF55681; Class II aaRS and biotin synthetases; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Magnesium; Metal-binding; Nucleotide-binding; Protein biosynthesis;
KW Reference proteome.
FT CHAIN 1..438
FT /note="Aspartate--tRNA(Asp) ligase"
FT /id="PRO_0000111005"
FT REGION 192..195
FT /note="Aspartate"
FT BINDING 170
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT BINDING 214..216
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 214
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT BINDING 222..224
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 361
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 361
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 361
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT BINDING 364
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT BINDING 364
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 368
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT BINDING 409..412
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT SITE 26
FT /note="Important for tRNA discrimination"
FT SITE 85
FT /note="Important for tRNA discrimination"
FT MUTAGEN 26
FT /note="W->H: Gains the ability to form Asp-tRNA(Asn) in
FT vitro. Only 2-fold decrease in catalytic efficiency for
FT Asp-tRNA(Asp) synthesis."
FT /evidence="ECO:0000269|PubMed:12730374"
FT MUTAGEN 85
FT /note="K->P: Gains the ability to form Asp-tRNA(Asn) in
FT vitro, and is impaired in its ability to synthesize Asp-
FT tRNA(Asp) due to a 8-fold decrease in affinity for
FT tRNA(Asp)."
FT /evidence="ECO:0000269|PubMed:12730374"
FT CONFLICT 413
FT /note="L -> V (in Ref. 1; BAA08115)"
FT /evidence="ECO:0000305"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 12..14
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 18..31
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 34..41
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 44..51
FT /evidence="ECO:0007829|PDB:3NEM"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 57..62
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 71..80
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 87..99
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 117..122
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 124..127
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 131..153
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 163..167
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 177..180
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 183..187
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 192..197
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 205..213
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 225..236
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 240..261
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 263..268
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 282..284
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 285..294
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 307..321
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 324..330
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 333..335
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 344..346
FT /evidence="ECO:0007829|PDB:3NEN"
FT STRAND 349..357
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 360..368
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 372..381
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 386..389
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 390..394
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 403..409
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 410..417
FT /evidence="ECO:0007829|PDB:3NEM"
FT HELIX 423..426
FT /evidence="ECO:0007829|PDB:3NEM"
FT STRAND 427..429
FT /evidence="ECO:0007829|PDB:3NEM"
SQ SEQUENCE 438 AA; 50910 MW; E03C8766ADD2209A CRC64;
MYRTHYSSEI TEELNGQKVK VAGWVWEVKD LGGIKFLWIR DRDGIVQITA PKKKVDPELF
KLIPKLRSED VVAVEGVVNF TPKAKLGFEI LPEKIVVLNR AETPLPLDPT GKVKAELDTR
LDNRFMDLRR PEVMAIFKIR SSVFKAVRDF FHENGFIEIH TPKIIATATE GGTELFPMKY
FEEDAFLAQS PQLYKQIMMA SGLDRVYEIA PIFRAEEHNT TRHLNEAWSI DSEMAFIEDE
EEVMSFLERL VAHAINYVRE HNAKELDILN FELEEPKLPF PRVSYDKALE ILGDLGKEIP
WGEDIDTEGE RLLGKYMMEN ENAPLYFLYQ YPSEAKPFYI MKYDNKPEIC RAFDLEYRGV
EISSGGQREH RHDILVEQIK EKGLNPESFE FYLKAFRYGM PPHGGFGLGA ERLIKQMLDL
PNIREVILFP RDRRRLTP
//
