SYS2_METBU
ID SYS2_METBU Reviewed; 502 AA.
AC Q12TN5;
DT 01-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=Type-2 serine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_01278};
DE EC=6.1.1.11 {ECO:0000255|HAMAP-Rule:MF_01278};
DE AltName: Full=Seryl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_01278};
DE Short=SerRS {ECO:0000255|HAMAP-Rule:MF_01278};
DE AltName: Full=Seryl-tRNA(Ser/Sec) synthetase {ECO:0000255|HAMAP-Rule:MF_01278};
GN Name=serS {ECO:0000255|HAMAP-Rule:MF_01278}; OrderedLocusNames=Mbur_2337;
OS Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 /
OS ACE-M).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanococcoides.
OX NCBI_TaxID=259564;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 6242 / NBRC 107633 / OCM 468 / ACE-M;
RX PubMed=19404327; DOI=10.1038/ismej.2009.45;
RA Allen M.A., Lauro F.M., Williams T.J., Burg D., Siddiqui K.S.,
RA De Francisci D., Chong K.W., Pilak O., Chew H.H., De Maere M.Z., Ting L.,
RA Katrib M., Ng C., Sowers K.R., Galperin M.Y., Anderson I.J., Ivanova N.,
RA Dalin E., Martinez M., Lapidus A., Hauser L., Land M., Thomas T.,
RA Cavicchioli R.;
RT "The genome sequence of the psychrophilic archaeon, Methanococcoides
RT burtonii: the role of genome evolution in cold adaptation.";
RL ISME J. 3:1012-1035(2009).
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:0000255|HAMAP-Rule:MF_01278}.
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 Evidence={ECO:0000255|HAMAP-Rule:MF_01278};
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:0000255|HAMAP-Rule:MF_01278};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01278};
CC Note=Binds 1 Zn(2+) ion per subunit. This ion is coordinated with 2
CC cysteines, 1 glutamate and a water molecule that dissociates from the
CC zinc ion to allow the coordination of the amino group of the serine
CC substrate, which is essential for catalysis. {ECO:0000255|HAMAP-
CC Rule:MF_01278};
CC -!- PATHWAY: Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec)
CC biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_01278}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01278}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01278}.
CC -!- DOMAIN: Consists of two distinct domains, a catalytic core and a N-
CC terminal extension that is presumably involved in tRNA binding.
CC {ECO:0000255|HAMAP-Rule:MF_01278}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type-2 seryl-tRNA synthetase subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_01278}.
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DR EMBL; CP000300; ABE53191.1; -; Genomic_DNA.
DR RefSeq; WP_011500326.1; NC_007955.1.
DR AlphaFoldDB; Q12TN5; -.
DR SMR; Q12TN5; -.
DR STRING; 259564.Mbur_2337; -.
DR PRIDE; Q12TN5; -.
DR EnsemblBacteria; ABE53191; ABE53191; Mbur_2337.
DR GeneID; 3998918; -.
DR KEGG; mbu:Mbur_2337; -.
DR HOGENOM; CLU_542524_0_0_2; -.
DR OMA; YYVCPPK; -.
DR OrthoDB; 9543at2157; -.
DR UniPathway; UPA00906; UER00895.
DR Proteomes; UP000001979; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004828; F:serine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016260; P:selenocysteine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0097056; P:selenocysteinyl-tRNA(Sec) biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006434; P:seryl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_01278; Ser_tRNA_synth_type2; 1.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR004503; Ser-tRNA-ligase_2_arc.
DR InterPro; IPR041293; SerS_tRNA-bd.
DR Pfam; PF18490; tRNA_bind_4; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
PE 3: Inferred from homology;
KW Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase; Metal-binding;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome; Zinc.
FT CHAIN 1..502
FT /note="Type-2 serine--tRNA ligase"
FT /id="PRO_0000286168"
FT BINDING 304
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 306
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 336..338
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 336
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 347..348
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 353..355
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 355
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 400
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 432
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 435
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 461
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 468
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
SQ SEQUENCE 502 AA; 57388 MW; E3DA16D5AC8FDF58 CRC64;
MELKFNLKGA FKTSTDPTGA KEVIAQYFDE ANNTILKKGA PEGQGAKITQ WDIVDGSIEL
TIESGRYVRA HDAIMRLKKP LAAKLGKEFR IGIRGVDVKK FTISMPAEGE IGNMNIPHVS
NISKVEGGLI LELNVGESEL ERRIPDRILT LMEEKVRAKD YGGKAEHWQI LWESDKKEHT
FAGDPTQEMM KHGWIKRGAS RGQWIHGPQS TKMFRTFEKI VYDELLEPLG YREMIFPKLV
PWEVWQKSGH AKGVYPEIYY VCPPKTRDPA YWEEVSDHYK VTHEVPTELI KSKIGDPIGG
LCYAQCPPFW MYLQGETIPT DEFPIKVFDK SGTSHRYESG GIHGIERVDE FHRVEIVWLG
TKEQVIETAR KLHERYMHIF NEILDLEWRK AWVTPWFMAQ EGLTGLSEQG EAGTTDYEAP
LPYRGDDGEW LEFQNVSING NKYPSGFNVK SQTGEELWSG CSGVGLERWA SAFFAQKGLD
PENWPEEFRK RVGEVPKGIR FL
