SYDND_THET8
ID SYDND_THET8 Reviewed; 422 AA.
AC Q5SIC2; Q9LCY8;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000255|HAMAP-Rule:MF_02075};
DE EC=6.1.1.23 {ECO:0000255|HAMAP-Rule:MF_02075};
DE AltName: Full=Aspartyl-tRNA synthetase 2;
DE Short=AspRS2;
DE AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_02075};
DE Short=ND-AspRS {ECO:0000255|HAMAP-Rule:MF_02075};
GN Name=aspS2; OrderedLocusNames=TTHA1452;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], GENE NAME, FUNCTION AS A
RP NON-DISCRIMINATING ASPRS, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND
RP KINETIC PARAMETERS.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=10727213; DOI=10.1021/bi992573y;
RA Becker H.D., Roy H., Moulinier L., Mazauric M.H., Keith G., Kern D.;
RT "Thermus thermophilus contains an eubacterial and an archaebacterial
RT aspartyl-tRNA synthetase.";
RL Biochemistry 39:3216-3230(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PROTEIN SEQUENCE OF 1-49, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS,
RP SUBUNIT, AND INDUCTION.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=9220965; DOI=10.1021/bi970392v;
RA Becker H.D., Reinbolt J., Kreutzer R., Giege R., Kern D.;
RT "Existence of two distinct aspartyl-tRNA synthetases in Thermus
RT thermophilus. Structural and biochemical properties of the two enzymes.";
RL Biochemistry 36:8785-8797(1997).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), AND SUBUNIT.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
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 X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEX WITH TRNA(ASN); GATA;
RP GATB AND GATC, IDENTIFICATION IN THE TRANSAMIDOSOME COMPLEX, AND SUBUNIT.
RX PubMed=20717102; DOI=10.1038/emboj.2010.192;
RA Blaise M., Bailly M., Frechin M., Behrens M.A., Fischer F., Oliveira C.L.,
RA Becker H.D., Pedersen J.S., Thirup S., Kern D.;
RT "Crystal structure of a transfer-ribonucleoprotein particle that promotes
RT asparagine formation.";
RL EMBO J. 29:3118-3129(2010).
CC -!- FUNCTION: Aspartyl-tRNA synthetase with relaxed tRNA specificity since
CC it is able to aspartylate not only its cognate tRNA(Asp) but also
CC tRNA(Asn) with similar efficiencies. Reaction proceeds in two steps: L-
CC aspartate is first activated by ATP to form Asp-AMP and then
CC transferred to the acceptor end of tRNA(Asp/Asn).
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-
CC aspartyl-tRNA(Asx); Xref=Rhea:RHEA:18349, Rhea:RHEA-COMP:9710,
CC Rhea:RHEA-COMP:9711, ChEBI:CHEBI:29991, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:78442, ChEBI:CHEBI:78516,
CC ChEBI:CHEBI:456215; EC=6.1.1.23; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_02075, ECO:0000269|PubMed:10727213,
CC ECO:0000269|PubMed:9220965};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3 uM for L-aspartate (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965};
CC KM=5 uM for L-aspartate (at 70 degrees Celsius)
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965};
CC KM=60 uM for ATP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965};
CC KM=33 uM for ATP (at 70 degrees Celsius)
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965};
CC KM=0.043 uM for tRNA(Asp) (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965};
CC KM=0.073 uM for tRNA(Asp) (at 70 degrees Celsius)
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965};
CC KM=0.063 uM for tRNA(Asn) (at 70 degrees Celsius)
CC {ECO:0000269|PubMed:10727213, ECO:0000269|PubMed:9220965};
CC Note=kcat is 0.09 sec(-1) for tRNA aspartylation at 37 degrees
CC Celsius and 0.24 sec(-1) at 70 degrees Celsius. kcat is 0.092 sec(-1)
CC for tRNA(Asn) aspartylation at 70 degrees Celsius.;
CC -!- SUBUNIT: Homodimer. Makes part of a ribonucleoprotein particle (RNP)
CC called transamidosome that allows channelling of the aa-tRNA from non-
CC discriminating aspartyl-tRNA synthetase active site to the GatCAB
CC amidotransferase site. The transamidosome complex is formed by two
CC GatCABs, one dimeric ND-AspRSs and two tRNAs(Asn) molecules.
CC {ECO:0000269|PubMed:12660169, ECO:0000269|PubMed:20717102,
CC ECO:0000269|PubMed:9220965}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_02075}.
CC -!- INDUCTION: Constitutively expressed in a constant ratio along the
CC growth of the bacterium. {ECO:0000269|PubMed:9220965}.
CC -!- MISCELLANEOUS: Aspartate mischarged on tRNA(Asn) is then converted into
CC asparagine by the tRNA-dependent amidotransferase GatCAB.
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; AF219996; AAF61689.1; -; Genomic_DNA.
DR EMBL; AP008226; BAD71275.1; -; Genomic_DNA.
DR RefSeq; WP_011228692.1; NC_006461.1.
DR RefSeq; YP_144718.1; NC_006461.1.
DR PDB; 1N9W; X-ray; 2.30 A; A/B=1-422.
DR PDB; 3KFU; X-ray; 3.00 A; A/B/C/D=1-422.
DR PDBsum; 1N9W; -.
DR PDBsum; 3KFU; -.
DR AlphaFoldDB; Q5SIC2; -.
DR SMR; Q5SIC2; -.
DR STRING; 300852.55772834; -.
DR EnsemblBacteria; BAD71275; BAD71275; BAD71275.
DR GeneID; 3169968; -.
DR KEGG; ttj:TTHA1452; -.
DR PATRIC; fig|300852.9.peg.1426; -.
DR eggNOG; COG0017; Bacteria.
DR HOGENOM; CLU_004553_2_1_0; -.
DR OMA; WVHEIRD; -.
DR PhylomeDB; Q5SIC2; -.
DR BRENDA; 6.1.1.12; 2305.
DR EvolutionaryTrace; Q5SIC2; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004815; F:aspartate-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0050560; F:aspartate-tRNA(Asn) ligase activity; IEA:UniProtKB-EC.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0006422; P:aspartyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.930.10; -; 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 PANTHER; PTHR43450; PTHR43450; 1.
DR Pfam; PF00152; tRNA-synt_2; 1.
DR Pfam; PF01336; tRNA_anti-codon; 1.
DR PRINTS; PR01042; TRNASYNTHASP.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00458; aspS_nondisc; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Direct protein sequencing; Ligase; Nucleotide-binding;
KW Protein biosynthesis; Reference proteome.
FT CHAIN 1..422
FT /note="Aspartate--tRNA(Asp/Asn) ligase"
FT /id="PRO_0000429273"
FT REGION 180..183
FT /note="Aspartate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 158
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 201..203
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 201
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 209..211
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 345
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 348
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 352
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT BINDING 393..396
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT SITE 26
FT /note="Interaction with tRNA"
FT SITE 44
FT /note="Interaction with tRNA"
FT SITE 68
FT /note="Interaction with tRNA"
FT SITE 72
FT /note="Important for tRNA non-discrimination"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02075"
FT SITE 76
FT /note="Interaction with tRNA"
FT HELIX 5..10
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 14..27
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 29..38
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 41..49
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 58..67
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 74..86
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:3KFU"
FT HELIX 107..110
FT /evidence="ECO:0007829|PDB:3KFU"
FT HELIX 112..115
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 119..141
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 191..198
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 215..223
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 227..248
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 250..255
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 264..266
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 269..271
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 272..281
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 293..306
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 310..315
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 319..321
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 332..341
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 344..352
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 356..365
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 370..373
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 374..377
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 378..381
FT /evidence="ECO:0007829|PDB:1N9W"
FT STRAND 386..393
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 394..401
FT /evidence="ECO:0007829|PDB:1N9W"
FT HELIX 407..410
FT /evidence="ECO:0007829|PDB:1N9W"
SQ SEQUENCE 422 AA; 48329 MW; 1C02F7D83F433490 CRC64;
MRVLVRDLKA HVGQEVELLG FLHWRRDLGR IQFLLLRDRS GVVQVVTGGL KLPLPESALR
VRGLVVENAK APGGLEVQAK EVEVLSPALE PTPVEIPKEE WRANPDTLLE YRYVTLRGEK
ARAPLKVQAA LVRGFRRYLD RQDFTEIFTP KVVRAGAEGG SGLFGVDYFE KRAYLAQSPQ
LYKQIMVGVF ERVYEVAPVW RMEEHHTSRH LNEYLSLDVE MGFIADEEDL MRLEEALLAE
MLEEALNTAG DEIRLLGATW PSFPQDIPRL THAEAKRILK EELGYPVGQD LSEEAERLLG
EYAKERWGSD WLFVTRYPRS VRPFYTYPEE DGTTRSFDLL FRGLEITSGG QRIHRYEELL
ESLKAKGMDP EAFHGYLEVF KYGMPPHGGF AIGAERLTQK LLGLPNVRYA RAFPRDRHRL
TP
