SYSC_ARATH
ID SYSC_ARATH Reviewed; 451 AA.
AC Q39230;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Serine--tRNA ligase, cytoplasmic {ECO:0000305};
DE EC=6.1.1.11 {ECO:0000305};
DE AltName: Full=Seryl-tRNA synthetase {ECO:0000305};
DE Short=SerRS {ECO:0000305};
DE AltName: Full=Seryl-tRNA(Ser/Sec) synthetase {ECO:0000305};
GN OrderedLocusNames=At5g27470; ORFNames=F21A20_180;
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].
RC STRAIN=cv. Columbia;
RA Peeters N.M., Small I.D.;
RT "A cDNA clone encoding Arabidopsis thaliana seryl-tRNA synthetase.";
RL (er) Plant Gene Register PGR96-047(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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 X-RAY CRYSTALLOGRAPHY (2.34 ANGSTROMS) OF 3-451, DISULFIDE BOND,
RP HOMODIMERIZATION, AND SUBUNIT.
RX PubMed=30570212; DOI=10.1111/febs.14735;
RA Kekez M., Zanki V., Kekez I., Baranasic J., Hodnik V., Duchene A.M.,
RA Anderluh G., Gruic-Sovulj I., Matkovic-Calogovic D., Weygand-Durasevic I.,
RA Rokov-Plavec J.;
RT "Arabidopsis seryl-tRNA synthetase: the first crystal structure and novel
RT protein interactor of plant aminoacyl-tRNA synthetase.";
RL FEBS J. 286:536-554(2019).
CC -!- FUNCTION: Catalyzes the attachment of serine to tRNA(Ser). Is also able
CC to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-
CC seryl-tRNA(Sec), which will be further converted into selenocysteinyl-
CC tRNA(Sec). {ECO:0000250|UniProtKB:P0A8L1}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-
CC seryl-tRNA(Ser); Xref=Rhea:RHEA:12292, Rhea:RHEA-COMP:9669,
CC Rhea:RHEA-COMP:9703, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:33384, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78533, ChEBI:CHEBI:456215; EC=6.1.1.11;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-
CC seryl-tRNA(Sec); Xref=Rhea:RHEA:42580, Rhea:RHEA-COMP:9742,
CC Rhea:RHEA-COMP:10128, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:33384, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78533, ChEBI:CHEBI:456215; EC=6.1.1.11;
CC -!- PATHWAY: Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec)
CC biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1.
CC -!- SUBUNIT: Homodimer (PubMed:30570212). The tRNA molecule binds across
CC the dimer (Probable). {ECO:0000269|PubMed:30570212,
CC ECO:0000305|PubMed:30570212}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000305|PubMed:16251277,
CC ECO:0000305|PubMed:16297076}.
CC -!- DOMAIN: Consists of two distinct domains, a catalytic core and a N-
CC terminal extension that is involved in tRNA binding. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type-1 seryl-tRNA synthetase subfamily. {ECO:0000305}.
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DR EMBL; Z70313; CAA94388.1; -; mRNA.
DR EMBL; AC007123; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93692.1; -; Genomic_DNA.
DR EMBL; AF360352; AAK28648.1; -; mRNA.
DR EMBL; AY051054; AAK93731.1; -; mRNA.
DR PIR; S71293; S71293.
DR RefSeq; NP_198099.1; NM_122629.3.
DR PDB; 6GIR; X-ray; 2.34 A; A=3-451.
DR PDBsum; 6GIR; -.
DR AlphaFoldDB; Q39230; -.
DR SMR; Q39230; -.
DR BioGRID; 18080; 10.
DR STRING; 3702.AT5G27470.1; -.
DR iPTMnet; Q39230; -.
DR PaxDb; Q39230; -.
DR PRIDE; Q39230; -.
DR ProteomicsDB; 233027; -.
DR DNASU; 832806; -.
DR EnsemblPlants; AT5G27470.1; AT5G27470.1; AT5G27470.
DR GeneID; 832806; -.
DR Gramene; AT5G27470.1; AT5G27470.1; AT5G27470.
DR KEGG; ath:AT5G27470; -.
DR Araport; AT5G27470; -.
DR TAIR; locus:2146400; AT5G27470.
DR eggNOG; KOG2509; Eukaryota.
DR HOGENOM; CLU_023797_0_1_1; -.
DR InParanoid; Q39230; -.
DR OMA; SPCFRRE; -.
DR OrthoDB; 726296at2759; -.
DR PhylomeDB; Q39230; -.
DR UniPathway; UPA00906; UER00895.
DR PRO; PR:Q39230; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q39230; baseline and differential.
DR Genevisible; Q39230; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004828; F:serine-tRNA ligase activity; IBA:GO_Central.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0097056; P:selenocysteinyl-tRNA(Sec) biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006434; P:seryl-tRNA aminoacylation; IBA:GO_Central.
DR CDD; cd00770; SerRS_core; 1.
DR Gene3D; 1.10.287.40; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR InterPro; IPR002314; aa-tRNA-synt_IIb.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR002317; Ser-tRNA-ligase_type_1.
DR InterPro; IPR015866; Ser-tRNA-synth_1_N.
DR InterPro; IPR042103; SerRS_1_N_sf.
DR InterPro; IPR033729; SerRS_core.
DR InterPro; IPR010978; tRNA-bd_arm.
DR PANTHER; PTHR11778; PTHR11778; 1.
DR Pfam; PF02403; Seryl_tRNA_N; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR PIRSF; PIRSF001529; Ser-tRNA-synth_IIa; 1.
DR PRINTS; PR00981; TRNASYNTHSER.
DR SUPFAM; SSF46589; SSF46589; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00414; serS; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Disulfide bond; Ligase; Nucleotide-binding; Protein biosynthesis;
KW Reference proteome.
FT CHAIN 1..451
FT /note="Serine--tRNA ligase, cytoplasmic"
FT /id="PRO_0000122195"
FT BINDING 238..240
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 269..271
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 285
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 292
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 358..361
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 396
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT DISULFID 213..244
FT /evidence="ECO:0000269|PubMed:30570212,
FT ECO:0007744|PDB:6GIR"
FT HELIX 4..7
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 14..25
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 31..60
FT /evidence="ECO:0007829|PDB:6GIR"
FT TURN 61..64
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 76..105
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 122..124
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 139..141
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 146..153
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 158..165
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 175..193
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 203..206
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 207..210
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 233..235
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 240..245
FT /evidence="ECO:0007829|PDB:6GIR"
FT TURN 246..249
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 254..256
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 258..268
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 282..284
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 286..297
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 299..302
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 303..321
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 326..330
FT /evidence="ECO:0007829|PDB:6GIR"
FT TURN 333..335
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 341..350
FT /evidence="ECO:0007829|PDB:6GIR"
FT TURN 351..354
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 355..364
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 368..372
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 391..399
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 400..410
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 414..418
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 421..423
FT /evidence="ECO:0007829|PDB:6GIR"
FT HELIX 425..427
FT /evidence="ECO:0007829|PDB:6GIR"
FT STRAND 432..434
FT /evidence="ECO:0007829|PDB:6GIR"
SQ SEQUENCE 451 AA; 51629 MW; B13D71EF87236AAF CRC64;
MLDINLFREE KGNNPEIIRE SQRRRFASVE IVDEIIKLDK EWRQRQFEVD SFRKEFNKLN
KQVAQLKIKK EDASEIIQQT EKNKQDSTAK EAEVREAYAA LKAKLEQVGN LVHDSVPVDK
DEANNLVIKL WGEKRFSTPG LKLKNHVDLV ELLGIADTKR GAEIAGARGF FLKGDGLMLN
QALINFGLTF LKKRGFTGLQ PPFFMRKDVM AKCAQLAQFD EELYKVTGEG DDKYLIATAE
QPLCAYHIDE WIHPTELPLR YAGYSSCFRK EAGSHGRDTL GIFRVHQFEK IEQFCITGPN
ENASWEMLDE MMKNSEDFYQ ALKLPYQIVS IVSGALNDAA AKKYDLEAWF PSSETFRELV
SCSNCTDYQA RRLEIRYGQK KSNEQTKQYV HMLNSTLTAT ERTICCILEN YQREDGVDIP
EVLQPFMGGE TFLPFKAKPV VADTKGKKSK A
