SYKM_ARATH
ID SYKM_ARATH Reviewed; 602 AA.
AC Q9LJE2;
DT 22-JUL-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Lysine--tRNA ligase, chloroplastic/mitochondrial {ECO:0000305};
DE EC=6.1.1.6 {ECO:0000305};
DE AltName: Full=Lysyl-tRNA synthetase {ECO:0000305};
DE Short=LysRS {ECO:0000305};
DE AltName: Full=Lysyl-tRNA synthetase 2 {ECO:0000305};
DE Short=AtKRS-2 {ECO:0000305};
DE AltName: Full=Protein OVULE ABORTION 5 {ECO:0000303|PubMed:16297076};
DE Flags: Precursor;
GN Name=OVA5 {ECO:0000303|PubMed:16297076};
GN OrderedLocusNames=At3g13490 {ECO:0000312|Araport:AT3G13490};
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
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=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 [4]
RP DISRUPTION PHENOTYPE.
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 [5]
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).
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. {ECO:0000250|UniProtKB:Q15046}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-
CC tRNA(Lys); Xref=Rhea:RHEA:20792, Rhea:RHEA-COMP:9696, Rhea:RHEA-
CC COMP:9697, ChEBI:CHEBI:30616, ChEBI:CHEBI:32551, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78529, ChEBI:CHEBI:456215; EC=6.1.1.6;
CC Evidence={ECO:0000305};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000250|UniProtKB:Q15046};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:16251277}. Mitochondrion
CC {ECO:0000269|PubMed:16251277}.
CC -!- DISRUPTION PHENOTYPE: Lethal. In heterozygous plants, aborted ovules.
CC {ECO:0000269|PubMed:16297076}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
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DR EMBL; AP000603; BAB01756.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75364.1; -; Genomic_DNA.
DR EMBL; BT002317; AAN86150.1; -; mRNA.
DR RefSeq; NP_187958.1; NM_112195.3.
DR AlphaFoldDB; Q9LJE2; -.
DR SMR; Q9LJE2; -.
DR IntAct; Q9LJE2; 1.
DR STRING; 3702.AT3G13490.1; -.
DR PaxDb; Q9LJE2; -.
DR PRIDE; Q9LJE2; -.
DR ProteomicsDB; 234103; -.
DR EnsemblPlants; AT3G13490.1; AT3G13490.1; AT3G13490.
DR GeneID; 820551; -.
DR Gramene; AT3G13490.1; AT3G13490.1; AT3G13490.
DR KEGG; ath:AT3G13490; -.
DR Araport; AT3G13490; -.
DR TAIR; locus:2092850; AT3G13490.
DR eggNOG; KOG1885; Eukaryota.
DR HOGENOM; CLU_008255_6_0_1; -.
DR InParanoid; Q9LJE2; -.
DR OMA; GRFENQI; -.
DR OrthoDB; 837479at2759; -.
DR PhylomeDB; Q9LJE2; -.
DR PRO; PR:Q9LJE2; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LJE2; baseline and differential.
DR Genevisible; Q9LJE2; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; 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:0004824; F:lysine-tRNA ligase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IBA:GO_Central.
DR GO; GO:0048481; P:plant ovule development; IMP:TAIR.
DR CDD; cd00775; LysRS_core; 1.
DR CDD; cd04322; LysRS_N; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00252; Lys_tRNA_synth_class2; 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; IPR002313; Lys-tRNA-ligase_II.
DR InterPro; IPR044136; Lys-tRNA-ligase_II_N.
DR InterPro; IPR018149; Lys-tRNA-synth_II_C.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004365; NA-bd_OB_tRNA.
DR Pfam; PF00152; tRNA-synt_2; 1.
DR Pfam; PF01336; tRNA_anti-codon; 1.
DR PRINTS; PR00982; TRNASYNTHLYS.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00499; lysS_bact; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 2: Evidence at transcript level;
KW Aminoacyl-tRNA synthetase; ATP-binding; Calcium; Chloroplast; DNA-binding;
KW Ligase; Metal-binding; Mitochondrion; Nucleotide-binding; Plastid;
KW Protein biosynthesis; Reference proteome; Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000305"
FT CHAIN ?..602
FT /note="Lysine--tRNA ligase, chloroplastic/mitochondrial"
FT /evidence="ECO:0000305"
FT /id="PRO_0000433540"
FT DNA_BIND 136..214
FT /note="OB"
FT /evidence="ECO:0000255"
FT REGION 50..83
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 524..550
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 50..82
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 524..547
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 285
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 309
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 331..333
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 339..340
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 347
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 349
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 492
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 499..500
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 499
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 502
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 506
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 575..578
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
SQ SEQUENCE 602 AA; 67588 MW; 1A09E969319D8365 CRC64;
MEALKVWSLT ATPLKQLLRL SSSSTRLATT IYGRRSYHLS PALRCASAAS SSSSSATTAE
TSKPSGRNRR SASSSNSTSD REAIRSIRLK KVEELRGQGL EPYAYKWEKS HSANQLQEIY
KHLANGEESD NEIDCVSIAG RVVARRAFGK LAFLTLRDDS GTIQLYCEKE RLSDDQFEQL
KQFIDIGDIL GASGSMKRTE KGELSICVNS FSILTKSLLP LPDKYHGLTD IDKRYRQRYV
DMIANPEVAD VFRRRAKIVS EIRKTVESFG YLEVETPVLQ GAAGGAEARP FVTFHNSLGR
DLYLRIATEL HLKRMLVGGF EKVYEIGRIF RNEGISTRHN PEFTTIEMYE AYSDYHSMMD
MAELIVTQCS MAVNGKLTID YQGTEICLER PWRRETMHNL VKEITGINFS ELGEDLGNAK
DTVLLALQDV LEPKDKSGIR ACSSLGHLLN EIFEVVVEPK LVQPTFVLDY PIEISPLAKP
HRGNAGLTER FELFICGREM ANAFSELTDP VDQRTRLEEQ VRQHNAKRAE AVRESPEPNA
KKDDDDDESY EVTLDEDFLT ALEYGMPPAS GMGLGIDRLV MLLTNSASIR DVIAFPVLKL
QQ
