ID SYK_ORYSJ Reviewed; 602 AA.
AC Q6F2U9; A0A0P0VZQ1; Q10HI7;
DT 09-NOV-2004, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 27-MAR-2024, entry version 126.
DE RecName: Full=Lysine--tRNA ligase;
DE EC=6.1.1.6;
DE AltName: Full=Lysyl-tRNA synthetase;
DE Short=LysRS;
GN OrderedLocusNames=Os03g0586800 {ECO:0000312|EMBL:BAF12486.1},
GN LOC_Os03g38980 {ECO:0000312|EMBL:ABF97355.1}; ORFNames=OSJNBa0010D22.26;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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 -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
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DR EMBL; AC133003; AAT76338.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF97355.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF12486.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS85100.1; -; Genomic_DNA.
DR EMBL; AK063765; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015631466.1; XM_015775980.1.
DR AlphaFoldDB; Q6F2U9; -.
DR SMR; Q6F2U9; -.
DR BioGRID; 802382; 1.
DR STRING; 39947.Q6F2U9; -.
DR PaxDb; 39947-Q6F2U9; -.
DR EnsemblPlants; Os03t0586800-02; Os03t0586800-02; Os03g0586800.
DR GeneID; 4333345; -.
DR Gramene; Os03t0586800-02; Os03t0586800-02; Os03g0586800.
DR KEGG; osa:4333345; -.
DR eggNOG; KOG1885; Eukaryota.
DR HOGENOM; CLU_008255_6_0_1; -.
DR InParanoid; Q6F2U9; -.
DR OMA; TPWAPGM; -.
DR OrthoDB; 648039at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q6F2U9; OS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004824; F:lysine-tRNA ligase activity; IBA:GO_Central.
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; Nucleic acid-binding proteins; 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 NCBIfam; TIGR00499; lysS_bact; 1.
DR PANTHER; PTHR42918:SF9; LYSINE--TRNA LIGASE; 1.
DR PANTHER; PTHR42918; LYSYL-TRNA SYNTHETASE; 1.
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; SSF55681; Class II aaRS and biotin synthetases; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 2: Evidence at transcript level;
KW Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT CHAIN 1..602
FT /note="Lysine--tRNA ligase"
FT /id="PRO_0000152770"
FT REGION 1..78
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 27..58
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 300
FT /note="M -> T (in Ref. 5; AK063765)"
FT /evidence="ECO:0000305"
FT CONFLICT 458
FT /note="K -> R (in Ref. 5; AK063765)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 602 AA; 68387 MW; 5BEAEE23EE853C85 CRC64;
MAESGSSGLE EKLAGLSAGC GEEPQQLSKN AKKREEKRKK QEEERRLKEE EKKKKAAATA
AASGEPPKES AADDEEMDPT QYYENRLKAL DSLKATGVNP YPHKFLANIT VADYIEKYKS
MNVGDKLVDV TECLAGRIMT KRAQSSKLLF YDLYGGGEKV QVFADARTSE LEDNEFIKFH
STLKRGDIVG VCGYPGKSKR GELSIFPKKI VVLSPCLHMM PRQKSEGSAV PTPWAPGMGR
NIEKYVLRDQ ETRYRQRYLD LMVNHEVRHI FKTRSKVVSF IRKFLDGLDF LEVETPMMNM
IAGGAAARPF VTHHNELNMR LYMRIAPELY LKELVVGGLD RVYEIGKQFR NEGIDLTHNP
EFTTCEFYMA YADYNDLIEL TETMLSGMVK ELTGGYKIKY HANGVEKPPI EIDFTPPFRK
IDMIEELEAM AKLNIPKDLS SDEANKYLID ACAKYDVKCP PPQTTTRLLD KLVGHFLEET
CVNPTFIINH PEIMSPLAKW HRSRPGLTER FELFVNKHEV CNAYTELNDP VVQRQRFEEQ
LKDRQSGDDE AMALDETFCT ALEYGLPPTG GWGLGIDRLT MLLTDSQNIK EVLLFPAMKP
QD
//
