SYDC_YEAST
ID SYDC_YEAST Reviewed; 557 AA.
AC P04802; D6VXY6;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 223.
DE RecName: Full=Aspartate--tRNA ligase, cytoplasmic;
DE EC=6.1.1.12;
DE AltName: Full=Aspartyl-tRNA synthetase;
DE Short=AspRS;
GN Name=DPS1; Synonyms=APS, APS1; OrderedLocusNames=YLL018C; ORFNames=L1295;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=3278298; DOI=10.1093/nar/16.3.1212;
RA Reid G.A.;
RT "Sequence polymorphisms in the yeast gene encoding aspartyl tRNA
RT synthase.";
RL Nucleic Acids Res. 16:1212-1212(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3513127; DOI=10.1093/nar/14.4.1657;
RA Sellami M., Fasiolo F., Dirheimer G., Ebel J.-P., Gangloff J.;
RT "Nucleotide sequence of the gene coding for yeast cytoplasmic aspartyl-tRNA
RT synthetase (APS); mapping of the 5' and 3' termini of AspRS mRNA.";
RL Nucleic Acids Res. 14:1657-1666(1986).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9046100;
RX DOI=10.1002/(sici)1097-0061(199702)13:2<183::aid-yea65>3.0.co;2-v;
RA Purnelle B., Goffeau A.;
RT "The sequence of 32kb on the left arm of yeast chromosome XII reveals six
RT known genes, a new member of the seripauperins family and a new ABC
RT transporter homologous to the human multidrug resistance protein.";
RL Yeast 13:183-188(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [6]
RP PROTEIN SEQUENCE OF 2-557.
RX PubMed=3902099; DOI=10.1016/s0300-9084(85)80200-5;
RA Amiri I., Mejdoub H., Hounwanou N., Boulanger Y., Reinbolt J.;
RT "The complete amino acid sequence of cytoplasmic aspartyl-tRNA synthetase
RT from Saccharomyces cerevisiae.";
RL Biochimie 67:607-613(1985).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-81.
RC STRAIN=ATCC 90840 / EAY235 / FY23;
RX PubMed=8810043;
RX DOI=10.1002/(sici)1097-0061(19960615)12:7<693::aid-yea956>3.0.co;2-g;
RA Miosga T., Zimmermann F.K.;
RT "Sequence analysis of the CEN12 region of Saccharomyces cerevisiae on a
RT 43.7 kb fragment of chromosome XII including an open reading frame
RT homologous to the human cystic fibrosis transmembrane conductance regulator
RT protein CFTR.";
RL Yeast 12:693-708(1996).
RN [8]
RP PARTIAL PROTEIN SEQUENCE, AND MUTAGENESIS.
RX PubMed=2021621; DOI=10.1021/bi00231a026;
RA Gasparini S., Vincendon P., Eriani G., Gangloff J., Boulanger Y.,
RA Reinbolt J., Kern D.;
RT "Identification of structurally and functionally important histidine
RT residues in cytoplasmic aspartyl-tRNA synthetase from Saccharomyces
RT cerevisiae.";
RL Biochemistry 30:4284-4289(1991).
RN [9]
RP MUTAGENESIS OF PRO-273.
RX PubMed=8248175; DOI=10.1073/pnas.90.22.10816;
RA Eriani G., Cavarelli J., Martin F., Dirheimer G., Moras D., Gangloff J.;
RT "Role of dimerization in yeast aspartyl-tRNA synthetase and importance of
RT the class II invariant proline.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:10816-10820(1993).
RN [10]
RP ACETYLATION AT SER-2.
RX PubMed=9298649; DOI=10.1002/elps.1150180810;
RA Garrels J.I., McLaughlin C.S., Warner J.R., Futcher B., Latter G.I.,
RA Kobayashi R., Schwender B., Volpe T., Anderson D.S., Mesquita-Fuentes R.,
RA Payne W.E.;
RT "Proteome studies of Saccharomyces cerevisiae: identification and
RT characterization of abundant proteins.";
RL Electrophoresis 18:1347-1360(1997).
RN [11]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-301, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-546, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-301 AND SER-502, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-301 AND SER-502, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RX PubMed=2047877; DOI=10.1126/science.2047877;
RA Ruff M., Krishnaswamy S., Boeglin M., Poterszman A., Mitschler A.,
RA Podjarny A., Rees B., Thierry J.-C., Moras D.;
RT "Class II aminoacyl transfer RNA synthetases: crystal structure of yeast
RT aspartyl-tRNA synthetase complexed with tRNA(Asp).";
RL Science 252:1682-1689(1991).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), AND MUTAGENESIS.
RX PubMed=8313877; DOI=10.1002/j.1460-2075.1994.tb06265.x;
RA Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A.,
RA Martin F., Gangloff J., Thierry J.-C., Moras D.;
RT "The active site of yeast aspartyl-tRNA synthetase: structural and
RT functional aspects of the aminoacylation reaction.";
RL EMBO J. 13:327-337(1994).
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;
CC -!- SUBUNIT: Homodimer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- MISCELLANEOUS: Present with 5750 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type 2 subfamily. {ECO:0000305}.
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DR EMBL; X03606; CAA27269.1; -; Genomic_DNA.
DR EMBL; X06665; CAA29865.1; -; Genomic_DNA.
DR EMBL; X97560; CAA66172.1; -; Genomic_DNA.
DR EMBL; Z73123; CAA97464.1; -; Genomic_DNA.
DR EMBL; Z73122; CAA97463.1; -; Genomic_DNA.
DR EMBL; X91488; CAA62772.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09302.1; -; Genomic_DNA.
DR PIR; A23508; SYBYDC.
DR RefSeq; NP_013083.1; NM_001181838.1.
DR PDB; 1ASY; X-ray; 2.90 A; A/B=68-557.
DR PDB; 1ASZ; X-ray; 3.00 A; A/B=68-557.
DR PDB; 1EOV; X-ray; 2.30 A; A=71-557.
DR PDBsum; 1ASY; -.
DR PDBsum; 1ASZ; -.
DR PDBsum; 1EOV; -.
DR AlphaFoldDB; P04802; -.
DR SMR; P04802; -.
DR BioGRID; 31235; 84.
DR DIP; DIP-4093N; -.
DR IntAct; P04802; 17.
DR MINT; P04802; -.
DR STRING; 4932.YLL018C; -.
DR CarbonylDB; P04802; -.
DR iPTMnet; P04802; -.
DR MaxQB; P04802; -.
DR PaxDb; P04802; -.
DR PRIDE; P04802; -.
DR EnsemblFungi; YLL018C_mRNA; YLL018C; YLL018C.
DR GeneID; 850643; -.
DR KEGG; sce:YLL018C; -.
DR SGD; S000003941; DPS1.
DR VEuPathDB; FungiDB:YLL018C; -.
DR eggNOG; KOG0556; Eukaryota.
DR GeneTree; ENSGT01030000234618; -.
DR HOGENOM; CLU_004553_2_1_1; -.
DR InParanoid; P04802; -.
DR OMA; WVHEIRD; -.
DR BioCyc; YEAST:G3O-32123-MON; -.
DR BRENDA; 6.1.1.12; 984.
DR SABIO-RK; P04802; -.
DR EvolutionaryTrace; P04802; -.
DR PRO; PR:P04802; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P04802; protein.
DR GO; GO:0017101; C:aminoacyl-tRNA synthetase multienzyme complex; IBA:GO_Central.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0004815; F:aspartate-tRNA ligase activity; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IDA:SGD.
DR GO; GO:0006422; P:aspartyl-tRNA aminoacylation; IDA:SGD.
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; Acetylation; Aminoacyl-tRNA synthetase; ATP-binding;
KW Cytoplasm; Direct protein sequencing; Ligase; Nucleotide-binding;
KW Phosphoprotein; Protein biosynthesis; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:3902099,
FT ECO:0000269|PubMed:9298649"
FT CHAIN 2..557
FT /note="Aspartate--tRNA ligase, cytoplasmic"
FT /id="PRO_0000111014"
FT REGION 1..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 303..306
FT /note="Aspartate"
FT /evidence="ECO:0000250"
FT COMPBIAS 28..71
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 281
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 325..327
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 325
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 333..335
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 478
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 481
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 485
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 528..531
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000269|PubMed:9298649"
FT MOD_RES 14
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 301
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 502
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 546
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358"
FT MUTAGEN 273
FT /note="P->G: Loss of activity; important for dimerization."
FT /evidence="ECO:0000269|PubMed:8248175"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:1EOV"
FT TURN 101..106
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 108..120
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 122..132
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 135..142
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 151..157
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 165..174
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 182..198
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 208..211
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 215..220
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 228..233
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 235..238
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 242..264
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 274..278
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 280..284
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 288..291
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 294..298
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 303..311
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 316..324
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 331..333
FT /evidence="ECO:0007829|PDB:1ASZ"
FT STRAND 336..346
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 352..372
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 374..383
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 393..395
FT /evidence="ECO:0007829|PDB:1ASY"
FT STRAND 398..401
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 402..411
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 418..420
FT /evidence="ECO:0007829|PDB:1ASY"
FT HELIX 424..437
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 441..446
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 450..452
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 461..463
FT /evidence="ECO:0007829|PDB:1ASZ"
FT STRAND 466..474
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 477..485
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 489..498
FT /evidence="ECO:0007829|PDB:1EOV"
FT TURN 506..508
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 509..515
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 522..528
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 529..536
FT /evidence="ECO:0007829|PDB:1EOV"
FT HELIX 542..545
FT /evidence="ECO:0007829|PDB:1EOV"
FT STRAND 546..548
FT /evidence="ECO:0007829|PDB:1ASY"
SQ SEQUENCE 557 AA; 63516 MW; 6656279B3E9011A5 CRC64;
MSQDENIVKA VEESAEPAQV ILGEDGKPLS KKALKKLQKE QEKQRKKEER ALQLEAEREA
REKKAAAEDT AKDNYGKLPL IQSRDSDRTG QKRVKFVDLD EAKDSDKEVL FRARVHNTRQ
QGATLAFLTL RQQASLIQGL VKANKEGTIS KNMVKWAGSL NLESIVLVRG IVKKVDEPIK
SATVQNLEIH ITKIYTISET PEALPILLED ASRSEAEAEA AGLPVVNLDT RLDYRVIDLR
TVTNQAIFRI QAGVCELFRE YLATKKFTEV HTPKLLGAPS EGGSSVFEVT YFKGKAYLAQ
SPQFNKQQLI VADFERVYEI GPVFRAENSN THRHMTEFTG LDMEMAFEEH YHEVLDTLSE
LFVFIFSELP KRFAHEIELV RKQYPVEEFK LPKDGKMVRL TYKEGIEMLR AAGKEIGDFE
DLSTENEKFL GKLVRDKYDT DFYILDKFPL EIRPFYTMPD PANPKYSNSY DFFMRGEEIL
SGAQRIHDHA LLQERMKAHG LSPEDPGLKD YCDGFSYGCP PHAGGGIGLE RVVMFYLDLK
NIRRASLFPR DPKRLRP
