SYCM_ARATH
ID SYCM_ARATH Reviewed; 563 AA.
AC F4IPY2; O82267; Q0WLQ1; Q93VX6;
DT 22-JUL-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=Cysteine--tRNA ligase, chloroplastic/mitochondrial {ECO:0000305};
DE EC=6.1.1.16 {ECO:0000305};
DE AltName: Full=Cysteinyl-tRNA synthetase {ECO:0000305};
DE Short=CysRS {ECO:0000305};
DE Flags: Precursor;
GN Name=SYCO {ECO:0000303|PubMed:10824085};
GN Synonyms=FIONA {ECO:0000303|PubMed:21135240};
GN OrderedLocusNames=At2g31170 {ECO:0000312|Araport:AT2G31170};
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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] OF 7-563 AND 71-563.
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 424-563.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SUBCELLULAR LOCATION.
RX PubMed=10824085; DOI=10.1007/s002390010044;
RA Peeters N.M., Chapron A., Giritch A., Grandjean O., Lancelin D., Lhomme T.,
RA Vivrel A., Small I.;
RT "Duplication and quadruplication of Arabidopsis thaliana cysteinyl- and
RT asparaginyl-tRNA synthetase genes of organellar origin.";
RL J. Mol. Evol. 50:413-423(2000).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=21135240; DOI=10.1073/pnas.1012795108;
RA Kagi C., Baumann N., Nielsen N., Stierhof Y.D., Gross-Hardt R.;
RT "The gametic central cell of Arabidopsis determines the lifespan of
RT adjacent accessory cells.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:22350-22355(2010).
CC -!- FUNCTION: Required for female gametophyte development. Is necessary for
CC the fusion of central cell nuclei and programmed cell death (PCD) of
CC the antipodals. {ECO:0000269|PubMed:21135240}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-
CC cysteinyl-tRNA(Cys); Xref=Rhea:RHEA:17773, Rhea:RHEA-COMP:9661,
CC Rhea:RHEA-COMP:9679, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:35235, ChEBI:CHEBI:78442, ChEBI:CHEBI:78517,
CC ChEBI:CHEBI:456215; EC=6.1.1.16; Evidence={ECO:0000305};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P21888};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:P21888};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:10824085}. Mitochondrion
CC {ECO:0000269|PubMed:10824085, ECO:0000269|PubMed:21135240}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences. {ECO:0000305};
CC Name=1;
CC IsoId=F4IPY2-1; Sequence=Displayed;
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality when homozygous.
CC {ECO:0000269|PubMed:21135240}.
CC -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD20662.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAK43958.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAM15026.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC005311; AAM15026.1; ALT_INIT; Genomic_DNA.
DR EMBL; AC006593; AAD20662.2; ALT_INIT; Genomic_DNA.
DR EMBL; CP002685; AEC08502.1; -; Genomic_DNA.
DR EMBL; AF370143; AAK43958.1; ALT_INIT; mRNA.
DR EMBL; AY051059; AAK93736.1; -; mRNA.
DR EMBL; AK230142; BAF01956.1; -; mRNA.
DR PIR; D84717; D84717.
DR RefSeq; NP_565717.2; NM_128673.5. [F4IPY2-1]
DR AlphaFoldDB; F4IPY2; -.
DR SMR; F4IPY2; -.
DR STRING; 3702.AT2G31170.1; -.
DR iPTMnet; F4IPY2; -.
DR PaxDb; F4IPY2; -.
DR PRIDE; F4IPY2; -.
DR ProteomicsDB; 233039; -. [F4IPY2-1]
DR EnsemblPlants; AT2G31170.1; AT2G31170.1; AT2G31170. [F4IPY2-1]
DR GeneID; 817673; -.
DR Gramene; AT2G31170.1; AT2G31170.1; AT2G31170. [F4IPY2-1]
DR KEGG; ath:AT2G31170; -.
DR Araport; AT2G31170; -.
DR TAIR; locus:2042521; AT2G31170.
DR eggNOG; KOG2007; Eukaryota.
DR HOGENOM; CLU_013528_0_1_1; -.
DR InParanoid; F4IPY2; -.
DR OMA; AKYWMHN; -.
DR PRO; PR:F4IPY2; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; F4IPY2; baseline and differential.
DR Genevisible; F4IPY2; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0004817; F:cysteine-tRNA ligase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042407; P:cristae formation; IMP:TAIR.
DR GO; GO:0006423; P:cysteinyl-tRNA aminoacylation; IBA:GO_Central.
DR GO; GO:0010197; P:polar nucleus fusion; IMP:TAIR.
DR GO; GO:0043067; P:regulation of programmed cell death; IMP:TAIR.
DR CDD; cd00672; CysRS_core; 1.
DR Gene3D; 3.40.50.620; -; 1.
DR HAMAP; MF_00041; Cys_tRNA_synth; 1.
DR InterPro; IPR015803; Cys-tRNA-ligase.
DR InterPro; IPR015273; Cys-tRNA-synt_Ia_DALR.
DR InterPro; IPR024909; Cys-tRNA/MSH_ligase.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR032678; tRNA-synt_1_cat_dom.
DR InterPro; IPR009080; tRNAsynth_Ia_anticodon-bd.
DR PANTHER; PTHR10890; PTHR10890; 1.
DR Pfam; PF09190; DALR_2; 1.
DR Pfam; PF01406; tRNA-synt_1e; 1.
DR PRINTS; PR00983; TRNASYNTHCYS.
DR SUPFAM; SSF47323; SSF47323; 1.
DR TIGRFAMs; TIGR00435; cysS; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Aminoacyl-tRNA synthetase; ATP-binding; Chloroplast;
KW Ligase; Metal-binding; Mitochondrion; Nucleotide-binding; Plastid;
KW Protein biosynthesis; Reference proteome; Transit peptide; Zinc.
FT TRANSIT 1..?
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000305"
FT CHAIN ?..563
FT /note="Cysteine--tRNA ligase, chloroplastic/mitochondrial"
FT /evidence="ECO:0000305"
FT /id="PRO_0000433558"
FT MOTIF 93..103
FT /note="'HIGH' region"
FT /evidence="ECO:0000305"
FT MOTIF 328..332
FT /note="'KMSKS' region"
FT /evidence="ECO:0000305"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P21888"
FT BINDING 271
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P21888"
FT BINDING 296
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P21888"
FT BINDING 300
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P21888"
FT BINDING 331
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
SQ SEQUENCE 563 AA; 63914 MW; 3A449280DA3FB30F CRC64;
MASSVLNLFK SCRPFTPIRF SSLPKSQFRI QFPLRPGKET QLRRCFTTLS SLTDGGAPIS
GGKELWLHNT MSRKKELFKP KVEGKVGMYV CGVTAYDLSH IGHARVYVTF DVLLRYLKHL
GYEVSYVRNF TDVDDKIIAR AKELEEDPIS LSRRFCEEFN RDMEQLQCLD PSVQPRVSDH
IPQIIDLIKQ ILDNGYAYKV DGDIYFSVDK FPTYGKLSGR KLEDNRAGER VAVDTRKKHP
ADFALWKAAK EGEPFWESPW GRGRPGWHIE CSAMSAAYLG YSFDIHGGGM DLVFPHHENE
IAQSCAACDS SNISYWIHNG FVTVDSEKMS KSLGNFFTIR QVIDLYHPLA LRLFLMGTHY
RSPINYSDFL LESASERIFY IYQTLHDCES ALGEKDSTFE NGSVPSDTLT SINTFRTEFV
ASMSDDLLTP VTLAAMSEPL KTINDLIHTR KGKKQARREE SLKALETTIR DVLTILGLMP
TSYSEVLEQL KEKALKRAGL KEEDVLQRVQ ERTDARKNKE YERSDAIRKD LAKVGIALMD
SPEGTTWRPA IPLALQEPVT TTP
