SYDC2_ARATH
ID SYDC2_ARATH Reviewed; 558 AA.
AC Q9M084; Q8VYA0;
DT 22-JUL-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Aspartate--tRNA ligase 2, cytoplasmic {ECO:0000305};
DE EC=6.1.1.12 {ECO:0000305};
DE AltName: Full=Aspartyl-tRNA synthetase {ECO:0000305};
DE Short=AspRS {ECO:0000305};
DE AltName: Full=Protein IMPAIRED IN BABA-INDUCED DISEASE IMMUNITY 1 {ECO:0000303|PubMed:24776930};
GN Name=IBI1 {ECO:0000303|PubMed:24776930};
GN OrderedLocusNames=At4g31180 {ECO:0000312|Araport:AT4G31180};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 107-558 AND 154-558.
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP SUBCELLULAR LOCATION.
RX PubMed=16297076; DOI=10.1111/j.1365-313x.2005.02580.x;
RA Berg M., Rogers R., Muralla R., Meinke D.;
RT "Requirement of aminoacyl-tRNA synthetases for gametogenesis and embryo
RT development in Arabidopsis.";
RL Plant J. 44:866-878(2005).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=16251277; DOI=10.1073/pnas.0504682102;
RA Duchene A.-M., Giritch A., Hoffmann B., Cognat V., Lancelin D.,
RA Peeters N.M., Zaepfel M., Marechal-Drouard L., Small I.D.;
RT "Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in
RT Arabidopsis thaliana.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:16484-16489(2005).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [8]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=24776930; DOI=10.1038/nchembio.1520;
RA Luna E., van Hulten M., Zhang Y., Berkowitz O., Lopez A., Petriacq P.,
RA Sellwood M.A., Chen B., Burrell M., van de Meene A., Pieterse C.M.,
RA Flors V., Ton J.;
RT "Plant perception of beta-aminobutyric acid is mediated by an aspartyl-tRNA
RT synthetase.";
RL Nat. Chem. Biol. 10:450-456(2014).
CC -!- FUNCTION: Catalyzes the specific attachment of an amino acid to its
CC cognate tRNA in a 2 step reaction: the amino acid (AA) is first
CC activated by ATP to form AA-AMP and then transferred to the acceptor
CC end of the tRNA (By similarity). Involved in the perception of beta-
CC aminobutyric acid (BABA) and required for BABA priming effect in
CC disease resistance (PubMed:24776930). {ECO:0000250|UniProtKB:P14868,
CC ECO:0000269|PubMed:24776930}.
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:0000305};
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:24776930,
CC ECO:0000305|PubMed:16251277, ECO:0000305|PubMed:16297076}. Endoplasmic
CC reticulum {ECO:0000269|PubMed:24776930}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type 2 subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL61938.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AL161578; CAB79836.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85872.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85873.1; -; Genomic_DNA.
DR EMBL; AK317607; BAH20270.1; -; mRNA.
DR EMBL; AY072331; AAL61938.1; ALT_SEQ; mRNA.
DR EMBL; BT002567; AAO00927.1; -; mRNA.
DR PIR; T10672; T10672.
DR RefSeq; NP_194847.3; NM_119268.4.
DR RefSeq; NP_849558.1; NM_179227.3.
DR AlphaFoldDB; Q9M084; -.
DR SMR; Q9M084; -.
DR STRING; 3702.AT4G31180.1; -.
DR iPTMnet; Q9M084; -.
DR PaxDb; Q9M084; -.
DR PRIDE; Q9M084; -.
DR ProteomicsDB; 233025; -.
DR EnsemblPlants; AT4G31180.1; AT4G31180.1; AT4G31180.
DR EnsemblPlants; AT4G31180.2; AT4G31180.2; AT4G31180.
DR GeneID; 829246; -.
DR Gramene; AT4G31180.1; AT4G31180.1; AT4G31180.
DR Gramene; AT4G31180.2; AT4G31180.2; AT4G31180.
DR KEGG; ath:AT4G31180; -.
DR Araport; AT4G31180; -.
DR TAIR; locus:2126306; AT4G31180.
DR eggNOG; KOG0556; Eukaryota.
DR HOGENOM; CLU_004553_2_1_1; -.
DR InParanoid; Q9M084; -.
DR OMA; WVHEIRD; -.
DR OrthoDB; 677307at2759; -.
DR PhylomeDB; Q9M084; -.
DR PRO; PR:Q9M084; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9M084; baseline and differential.
DR Genevisible; Q9M084; AT.
DR GO; GO:0017101; C:aminoacyl-tRNA synthetase multienzyme complex; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0004815; F:aspartate-tRNA ligase activity; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0006422; P:aspartyl-tRNA aminoacylation; IBA:GO_Central.
DR GO; GO:0050832; P:defense response to fungus; IMP:TAIR.
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 Acetylation; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW DNA-binding; Endoplasmic reticulum; Ligase; Magnesium; Metal-binding;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..558
FT /note="Aspartate--tRNA ligase 2, cytoplasmic"
FT /id="PRO_0000433560"
FT DNA_BIND 110..195
FT /note="OB"
FT /evidence="ECO:0000255"
FT REGION 1..57
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 308..311
FT /note="Aspartate"
FT /evidence="ECO:0000250"
FT COMPBIAS 1..19
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 20..57
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 286
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 330..332
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 330
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 338..340
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 481
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 481
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 481
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 484
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 484
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 488
FT /ligand="L-aspartate"
FT /ligand_id="ChEBI:CHEBI:29991"
FT /evidence="ECO:0000250"
FT BINDING 529..532
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 558 AA; 62918 MW; 598518C65AD9A4B3 CRC64;
MSSESEIPPL SSSTAAAEES GEKTSKKAAK KEAAKLEKLR RRQEQEEATR RTASISLEEN
DEFSNNYGDV TLTELQSSAD PKAGKWIEAV EGKEWTDVSD LVEEMLESEV LIRGRVHTNR
PTSNKLGFVV LRESGSTVQC VVSQSEKTKV GANMVKYLKQ LSRESFVDVI GVVTLPKEPL
TGTTQQVEIQ VRKVYCINKS LAKLPLSVED AARSEADIEA SLQTPSPAAR VNQDTRLNYR
VLDLRTPANQ AIFQLQYEVE YAFREKLRFK NFVGIHTPKL MAGSSEGGSA VFRLEYKGQP
ACLAQSPQLH KQMAICGDLR RVFEVGPVFR AEDSFTHRHL CEFVGLDVEM EIRKHYSEIM
DLVDELFVFI FTSLNERCKK ELQAVGKQYP FEPLKFLPKT LRLTFEEGVQ MLKEAGVEVD
PLGDLNTESE RKLGQLVLEK YNTEFYILHR YPKAVRPFYT MTCADNPLYS NSFDVFIRGE
EIISGAQRVH IPEVLEQRAG ECGIDVKTIS TYIDSFRYGA PLHGGFGVGL ERVVMLFCAL
NNIRKTSLFP RDPQRLSP
