SYKC_ARATH
ID SYKC_ARATH Reviewed; 626 AA.
AC Q9ZPI1;
DT 09-NOV-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Lysine--tRNA ligase, cytoplasmic {ECO:0000305};
DE EC=6.1.1.6 {ECO:0000269|PubMed:17425721};
DE AltName: Full=Lysyl-tRNA synthetase {ECO:0000305};
DE Short=LysRS {ECO:0000305};
DE AltName: Full=Lysyl-tRNA synthetase 1 {ECO:0000303|PubMed:17425721};
DE Short=AtKRS-1 {ECO:0000303|PubMed:17425721};
GN OrderedLocusNames=At3g11710; ORFNames=T19F11.11;
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 [MRNA].
RA Giritch A., Small I.D.;
RT "The Arabidopsis lysyl-tRNA synthetase: cDNA cloning and
RT characterisation.";
RL Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
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 [4]
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 [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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [8]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=17425721; DOI=10.1111/j.1365-313x.2007.03076.x;
RA Wu X.R., Kenzior A., Willmot D., Scanlon S., Chen Z., Topin A., He S.H.,
RA Acevedo A., Folk W.R.;
RT "Altered expression of plant lysyl tRNA synthetase promotes tRNA
RT misacylation and translational recoding of lysine.";
RL Plant J. 50:627-636(2007).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [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).
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). Promotes aminoacylation of non-cognate
CC tRNAs and translational recoding of lysine at nonsense codons
CC (PubMed:17425721). {ECO:0000250|UniProtKB:Q15046,
CC ECO:0000269|PubMed:17425721}.
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:0000269|PubMed:17425721};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000250|UniProtKB:Q15046};
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000305|PubMed:16251277,
CC ECO:0000305|PubMed:16297076}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
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DR EMBL; AF125574; AAD17333.1; -; mRNA.
DR EMBL; AC009918; AAF02138.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75086.1; -; Genomic_DNA.
DR EMBL; AY099551; AAM20403.1; -; mRNA.
DR EMBL; BT002123; AAN72134.1; -; mRNA.
DR RefSeq; NP_187777.1; NM_112003.4.
DR AlphaFoldDB; Q9ZPI1; -.
DR SMR; Q9ZPI1; -.
DR BioGRID; 5677; 19.
DR IntAct; Q9ZPI1; 1.
DR STRING; 3702.AT3G11710.1; -.
DR iPTMnet; Q9ZPI1; -.
DR MetOSite; Q9ZPI1; -.
DR PaxDb; Q9ZPI1; -.
DR PRIDE; Q9ZPI1; -.
DR ProteomicsDB; 233042; -.
DR EnsemblPlants; AT3G11710.1; AT3G11710.1; AT3G11710.
DR GeneID; 820343; -.
DR Gramene; AT3G11710.1; AT3G11710.1; AT3G11710.
DR KEGG; ath:AT3G11710; -.
DR Araport; AT3G11710; -.
DR TAIR; locus:2098348; AT3G11710.
DR eggNOG; KOG1885; Eukaryota.
DR HOGENOM; CLU_008255_6_0_1; -.
DR InParanoid; Q9ZPI1; -.
DR OMA; WAPGMGR; -.
DR OrthoDB; 837479at2759; -.
DR PhylomeDB; Q9ZPI1; -.
DR PRO; PR:Q9ZPI1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9ZPI1; baseline and differential.
DR Genevisible; Q9ZPI1; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA: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; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IBA:GO_Central.
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; IPR034762; Lys-tRNA-ligase_II_bac/euk.
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 PIRSF; PIRSF039101; LysRS2; 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 1: Evidence at protein level;
KW Acetylation; Aminoacyl-tRNA synthetase; ATP-binding; Calcium; Coiled coil;
KW Cytoplasm; DNA-binding; Ligase; Metal-binding; Nucleotide-binding;
KW Protein biosynthesis; Reference proteome.
FT CHAIN 1..626
FT /note="Lysine--tRNA ligase, cytoplasmic"
FT /id="PRO_0000152768"
FT DNA_BIND 141..217
FT /note="OB"
FT /evidence="ECO:0000255"
FT REGION 1..84
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 37..69
FT /evidence="ECO:0000255"
FT COMPBIAS 12..28
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 38..69
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 313
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 337
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 359..361
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 367..368
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 375
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 377
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 521
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 528..529
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 528
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 531
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 535
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT BINDING 584..587
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q15046"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 626 AA; 70888 MW; A0E9B774BF23220D CRC64;
MEGAADQTTK ALSELAMDSS TTLNAAESSA GDGAGPRSKN ALKKEQKMKQ KEEEKRRKDE
EKAEKAKQAP KASSQKAVAA DDEEMDATQY YENRLKYLAA EKAKGENPYP HKFAVSMSIP
KYIETYGSLN NGDHVENAEE SLAGRIMSKR SSSSKLFFYD LHGDDFKVQV MADASKSGLD
EAEFLKLHSN AKRGDIVGVI GFPGKTKRGE LSIFPRSFIL LSHCLHMMPR KADNVNAKKP
EIWVPGQTRN PEAYVLKDQE SRYRQRHLDM ILNVEVRQIF RTRAKIISYV RRFLDNKNFL
EVETPMMNMI AGGAAARPFV THHNDLDMRL YMRIAPELYL KQLIVGGLER VYEIGKQFRN
EGIDLTHNPE FTTCEFYMAF ADYNDLMEMT EVMLSGMVKE LTGGYKIKYN ANGYDKDPIE
IDFTPPFRRI EMIGELEKVA KLNIPKDLAS EEANKYLIDA CARFDVKCPP PQTTARLLDK
LVGEFLEPTC VNPTFIINQP EIMSPLAKWH RSKSGLTERF ELFINKHELC NAYTELNDPV
VQRQRFADQL KDRQSGDDEA MALDETFCNA LEYGLAPTGG WGLGIDRLSM LLTDSLNIKE
VLFFPAMRPP QEESAAAQAP LTEEKK
