SYDND_HELPY
ID SYDND_HELPY Reviewed; 577 AA.
AC P56459;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Aspartate--tRNA(Asp/Asn) ligase {ECO:0000255|HAMAP-Rule:MF_00044};
DE EC=6.1.1.23 {ECO:0000255|HAMAP-Rule:MF_00044};
DE AltName: Full=Aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044};
DE Short=AspRS {ECO:0000255|HAMAP-Rule:MF_00044};
DE AltName: Full=Non-discriminating aspartyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00044};
DE Short=ND-AspRS {ECO:0000255|HAMAP-Rule:MF_00044};
GN Name=aspS {ECO:0000255|HAMAP-Rule:MF_00044}; OrderedLocusNames=HP_0617;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
RN [2]
RP FUNCTION AS A NON-DISCRIMINATING ASPRS, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, KINETIC PARAMETERS, AND MUTAGENESIS OF LEU-81 AND LEU-86.
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=16800632; DOI=10.1021/bi060189c;
RA Chuawong P., Hendrickson T.L.;
RT "The nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori:
RT anticodon-binding domain mutations that impact tRNA specificity and
RT heterologous toxicity.";
RL Biochemistry 45:8079-8087(2006).
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). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over
CC tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first
CC activated by ATP to form Asp-AMP and then transferred to the acceptor
CC end of tRNA(Asp/Asn). {ECO:0000269|PubMed:16800632}.
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_00044, ECO:0000269|PubMed:16800632};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.77 uM for tRNA(Asp) {ECO:0000269|PubMed:16800632};
CC KM=0.83 uM for tRNA(Asn) {ECO:0000269|PubMed:16800632};
CC Note=kcat is 0.022 sec(-1) for tRNA(Asp) aspartylation and 0.014
CC sec(-1) for tRNA(Asn) aspartylation.;
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00044}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00044}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type 1 subfamily. {ECO:0000255|HAMAP-Rule:MF_00044}.
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DR EMBL; AE000511; AAD07682.1; -; Genomic_DNA.
DR PIR; A64597; A64597.
DR RefSeq; NP_207412.1; NC_000915.1.
DR RefSeq; WP_001256425.1; NC_018939.1.
DR PDB; 5GRO; X-ray; 2.00 A; A/B=1-104.
DR PDBsum; 5GRO; -.
DR AlphaFoldDB; P56459; -.
DR SMR; P56459; -.
DR DIP; DIP-3174N; -.
DR IntAct; P56459; 2.
DR MINT; P56459; -.
DR STRING; 85962.C694_03190; -.
DR PaxDb; P56459; -.
DR EnsemblBacteria; AAD07682; AAD07682; HP_0617.
DR KEGG; hpy:HP_0617; -.
DR PATRIC; fig|85962.47.peg.665; -.
DR eggNOG; COG0173; Bacteria.
DR OMA; YQLDVEM; -.
DR PhylomeDB; P56459; -.
DR BRENDA; 6.1.1.12; 2604.
DR Proteomes; UP000000429; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004815; F:aspartate-tRNA ligase activity; IBA:GO_Central.
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; IBA:GO_Central.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.1360.30; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00044; Asp_tRNA_synth_type1; 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; IPR004524; Asp-tRNA-ligase_1.
DR InterPro; IPR002312; Asp/Asn-tRNA-synth_IIb.
DR InterPro; IPR004115; GAD-like_sf.
DR InterPro; IPR029351; GAD_dom.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004365; NA-bd_OB_tRNA.
DR PANTHER; PTHR22594:SF5; PTHR22594:SF5; 1.
DR Pfam; PF02938; GAD; 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; SSF55261; SSF55261; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00459; aspS_bact; 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 Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT CHAIN 1..577
FT /note="Aspartate--tRNA(Asp/Asn) ligase"
FT /id="PRO_0000110883"
FT REGION 195..198
FT /note="Aspartate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 171
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 217..219
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 217
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 226
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 444
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 474
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 481
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT BINDING 526..529
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT SITE 30
FT /note="Important for tRNA non-discrimination"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT SITE 80
FT /note="Important for tRNA non-discrimination"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00044"
FT MUTAGEN 81
FT /note="L->N: Enhances enzyme specificity for tRNA(Asp) over
FT tRNA(Asn), by reducing enzyme's ability to misacylate
FT tRNA(Asn)."
FT /evidence="ECO:0000269|PubMed:16800632"
FT MUTAGEN 86
FT /note="L->M: Enhances enzyme specificity for tRNA(Asp) over
FT tRNA(Asn), by reducing enzyme's ability to misacylate
FT tRNA(Asn)."
FT /evidence="ECO:0000269|PubMed:16800632"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:5GRO"
FT HELIX 11..13
FT /evidence="ECO:0007829|PDB:5GRO"
FT STRAND 17..30
FT /evidence="ECO:0007829|PDB:5GRO"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:5GRO"
FT STRAND 43..49
FT /evidence="ECO:0007829|PDB:5GRO"
FT HELIX 56..59
FT /evidence="ECO:0007829|PDB:5GRO"
FT STRAND 67..76
FT /evidence="ECO:0007829|PDB:5GRO"
FT TURN 87..90
FT /evidence="ECO:0007829|PDB:5GRO"
FT STRAND 91..100
FT /evidence="ECO:0007829|PDB:5GRO"
SQ SEQUENCE 577 AA; 65602 MW; 29963C376EE9E68F CRC64;
MRSHFCTEIS EKDVGKIVKV AGWCNTYRDH GGVVFIDLRD KSGLVQLVCD PSSKAYEKAL
EVRSEFVLVA KGKVRLRGAG LENPKLKTGK IEIVLEELII ENKSATPPIE IGNKHVNEDL
RLKYRYLDLR SPNSYEIFKL RSEVALITRN TLAQKGFLEI ETPILSKTTP EGARDYLVPS
RVHEGEFFAL PQSPQLFKQL LMVGGMDRYF QIARCFRDED LRADRQPEFT QIDAEMSFCD
ENDVMGVVED LLQEIFKAVG HTISKPFKRM PYKEAMENYG SDKPDLRFEL PLIEVGDCFR
DSSNAIFSNT AKDPKNKRIK ALNVKGADAL FSRSVLKELE EFVRQFGAKG LAYLQIKEDE
IKGPLVKFLS EKGLKNILER TDAQVGDIVF FGAGDKKIVL DYMGRLRLKV AETLDLIDKD
ALNFLWVVNF PMFEKTENGY HAAHHPFTMP KNIECEDIEE VEAHAYDVVL NGVELGGGSI
RIHKEEMQKK VFEKINIHEE EAQKKFGFLL EALKFGAPPH GGFAIGFDRL IMLMTKSHSI
RDVIAFPKTQ KASCLLTNAP SPINEEQLRE LHIRLRK
