SYS_ECOLI
ID SYS_ECOLI Reviewed; 430 AA.
AC P0A8L1; P09156;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Serine--tRNA ligase;
DE EC=6.1.1.11 {ECO:0000269|PubMed:7537870};
DE AltName: Full=Seryl-tRNA synthetase;
DE Short=SerRS;
DE AltName: Full=Seryl-tRNA(Ser/Sec) synthetase;
GN Name=serS; OrderedLocusNames=b0893, JW0876;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3029694; DOI=10.1093/nar/15.3.1005;
RA Haertlein M., Madern D., Leberman R.;
RT "Cloning and characterization of the gene for Escherichia coli seryl-tRNA
RT synthetase.";
RL Nucleic Acids Res. 15:1005-1017(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 251-430.
RX PubMed=3062312; DOI=10.1111/j.1365-2958.1988.tb00090.x;
RA Bilous P.T., Cole S.T., Anderson W.F., Weiner J.H.;
RT "Nucleotide sequence of the dmsABC operon encoding the anaerobic
RT dimethylsulphoxide reductase of Escherichia coli.";
RL Mol. Microbiol. 2:785-795(1988).
RN [6]
RP FUNCTION AS A SERYL-TRNA(SEC) SYNTHETASE.
RX PubMed=2963963; DOI=10.1038/331723a0;
RA Leinfelder W., Zehelein E., Mandrand-Berthelot M.A., Boeck A.;
RT "Gene for a novel tRNA species that accepts L-serine and cotranslationally
RT inserts selenocysteine.";
RL Nature 331:723-725(1988).
RN [7]
RP REVIEW.
RX PubMed=1859832; DOI=10.1016/0167-4781(91)90168-l;
RA Leberman R., Haertlein M., Cusack S.;
RT "Escherichia coli seryl-tRNA synthetase: the structure of a class 2
RT aminoacyl-tRNA synthetase.";
RL Biochim. Biophys. Acta 1089:287-298(1991).
RN [8]
RP SUBUNIT, DOMAIN, AND CRYSTALLIZATION.
RX PubMed=8508916; DOI=10.1016/0014-5793(93)81386-e;
RA Price S., Cusack S., Borel F., Berthet-Colominas C., Leberman R.;
RT "Crystallization of the seryl-tRNA synthetase:tRNA(Ser) complex of
RT Escherichia coli.";
RL FEBS Lett. 324:167-170(1993).
RN [9]
RP FUNCTION, KINETIC PARAMETERS, AND DOMAIN.
RX PubMed=8065908; DOI=10.1093/nar/22.15.2963;
RA Borel F., Vincent C., Leberman R., Haertlein M.;
RT "Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal
RT domain in aminoacylation activity and specificity.";
RL Nucleic Acids Res. 22:2963-2969(1994).
RN [10]
RP FUNCTION, KINETIC PARAMETERS, MUTAGENESIS OF GLU-355, SUBUNIT, REACTION
RP MECHANISM, CATALYTIC ACTIVITY, AND DOMAIN.
RX PubMed=7537870; DOI=10.1093/nar/23.7.1113;
RA Vincent C., Borel F., Willison J.C., Leberman R., Haertlein M.;
RT "Seryl-tRNA synthetase from Escherichia coli: functional evidence for
RT cross-dimer tRNA binding during aminoacylation.";
RL Nucleic Acids Res. 23:1113-1118(1995).
RN [11]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=2205803; DOI=10.1038/347249a0;
RA Cusack S., Berthet-Colominas C., Haertlein M., Nassar N., Leberman R.;
RT "A second class of synthetase structure revealed by X-ray analysis of
RT Escherichia coli seryl-tRNA synthetase at 2.5 A.";
RL Nature 347:249-255(1990).
CC -!- FUNCTION: Catalyzes the attachment of serine to tRNA(Ser)
CC (PubMed:7537870). Is also able to aminoacylate tRNA(Sec) with serine,
CC to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further
CC converted into selenocysteinyl-tRNA(Sec). {ECO:0000269|PubMed:2963963,
CC ECO:0000269|PubMed:7537870, ECO:0000269|PubMed:8065908}.
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 Evidence={ECO:0000269|PubMed:7537870};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=64 uM for serine {ECO:0000269|PubMed:7537870,
CC ECO:0000269|PubMed:8065908};
CC KM=0.068 uM for ATP {ECO:0000269|PubMed:7537870,
CC ECO:0000269|PubMed:8065908};
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:7537870). The tRNA molecule binds across the
CC dimer, one part binds the N-terminus of the first SerRS subunit and the
CC other part to the active site of the second subunit (PubMed:7537870).
CC {ECO:0000269|PubMed:7537870, ECO:0000269|PubMed:8508916}.
CC -!- INTERACTION:
CC P0A8L1; P0A8L1: serS; NbExp=3; IntAct=EBI-548422, EBI-548422;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- DOMAIN: Consists of two distinct domains, a catalytic core and a N-
CC terminal extension that is involved in tRNA binding.
CC {ECO:0000269|PubMed:7537870, ECO:0000269|PubMed:8065908,
CC ECO:0000269|PubMed:8508916}.
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; X05017; CAA28673.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73979.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35625.1; -; Genomic_DNA.
DR EMBL; J03412; AAA83842.1; -; Genomic_DNA.
DR PIR; A26400; YSEC.
DR RefSeq; NP_415413.1; NC_000913.3.
DR RefSeq; WP_000886683.1; NZ_STEB01000006.1.
DR PDB; 6R1M; X-ray; 1.50 A; A/B=1-430.
DR PDB; 6R1O; X-ray; 2.60 A; A=1-430.
DR PDBsum; 6R1M; -.
DR PDBsum; 6R1O; -.
DR AlphaFoldDB; P0A8L1; -.
DR SMR; P0A8L1; -.
DR BioGRID; 4261485; 23.
DR BioGRID; 849880; 1.
DR DIP; DIP-35989N; -.
DR IntAct; P0A8L1; 16.
DR STRING; 511145.b0893; -.
DR BindingDB; P0A8L1; -.
DR ChEMBL; CHEMBL4295569; -.
DR SWISS-2DPAGE; P0A8L1; -.
DR jPOST; P0A8L1; -.
DR PaxDb; P0A8L1; -.
DR PRIDE; P0A8L1; -.
DR EnsemblBacteria; AAC73979; AAC73979; b0893.
DR EnsemblBacteria; BAA35625; BAA35625; BAA35625.
DR GeneID; 67414653; -.
DR GeneID; 945506; -.
DR KEGG; ecj:JW0876; -.
DR KEGG; eco:b0893; -.
DR PATRIC; fig|1411691.4.peg.1384; -.
DR EchoBASE; EB0940; -.
DR eggNOG; COG0172; Bacteria.
DR HOGENOM; CLU_023797_1_1_6; -.
DR InParanoid; P0A8L1; -.
DR OMA; SPCFRRE; -.
DR PhylomeDB; P0A8L1; -.
DR BioCyc; EcoCyc:SERS-MON; -.
DR BioCyc; MetaCyc:SERS-MON; -.
DR UniPathway; UPA00906; UER00895.
DR PRO; PR:P0A8L1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0004828; F:serine-tRNA ligase activity; IDA:UniProtKB.
DR GO; GO:0016260; P:selenocysteine biosynthetic process; IDA:EcoCyc.
DR GO; GO:0097056; P:selenocysteinyl-tRNA(Sec) biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006434; P:seryl-tRNA aminoacylation; IDA:UniProtKB.
DR CDD; cd00770; SerRS_core; 1.
DR Gene3D; 1.10.287.40; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00176; Ser_tRNA_synth_type1; 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; PTHR43697; PTHR43697; 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; Ligase;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT CHAIN 1..430
FT /note="Serine--tRNA ligase"
FT /id="PRO_0000122044"
FT BINDING 237..239
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 268..270
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 291
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 355..358
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 391
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT MUTAGEN 355
FT /note="E->Q: Loss of serine activation activity."
FT /evidence="ECO:0000269|PubMed:7537870"
FT HELIX 4..9
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 11..19
FT /evidence="ECO:0007829|PDB:6R1M"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 27..64
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 69..100
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 121..127
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 139..145
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 151..157
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 167..187
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 201..206
FT /evidence="ECO:0007829|PDB:6R1M"
FT TURN 210..213
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:6R1M"
FT TURN 227..229
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 232..234
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 239..243
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 250..252
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 258..267
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 279..283
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 285..296
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 301..318
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 323..327
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 330..332
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 338..347
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 348..350
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 352..361
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 365..370
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 373..375
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 382..384
FT /evidence="ECO:0007829|PDB:6R1M"
FT STRAND 386..394
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 395..405
FT /evidence="ECO:0007829|PDB:6R1M"
FT HELIX 417..422
FT /evidence="ECO:0007829|PDB:6R1M"
FT TURN 423..425
FT /evidence="ECO:0007829|PDB:6R1M"
SQ SEQUENCE 430 AA; 48414 MW; 87675745A512A626 CRC64;
MLDPNLLRNE PDAVAEKLAR RGFKLDVDKL GALEERRKVL QVKTENLQAE RNSRSKSIGQ
AKARGEDIEP LRLEVNKLGE ELDAAKAELD ALQAEIRDIA LTIPNLPADE VPVGKDENDN
VEVSRWGTPR EFDFEVRDHV TLGEMHSGLD FAAAVKLTGS RFVVMKGQIA RMHRALSQFM
LDLHTEQHGY SENYVPYLVN QDTLYGTGQL PKFAGDLFHT RPLEEEADTS NYALIPTAEV
PLTNLVRGEI IDEDDLPIKM TAHTPCFRSE AGSYGRDTRG LIRMHQFDKV EMVQIVRPED
SMAALEEMTG HAEKVLQLLG LPYRKIILCT GDMGFGACKT YDLEVWIPAQ NTYREISSCS
NVWDFQARRM QARCRSKSDK KTRLVHTLNG SGLAVGRTLV AVMENYQQAD GRIEVPEVLR
PYMNGLEYIG
