SYS2_METTH
ID SYS2_METTH Reviewed; 513 AA.
AC O27194; O30521;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Type-2 serine--tRNA ligase;
DE EC=6.1.1.11;
DE AltName: Full=Seryl-tRNA synthetase;
DE Short=SerRS;
DE AltName: Full=Seryl-tRNA(Ser/Sec) synthetase;
GN Name=serS; OrderedLocusNames=MTH_1122;
OS Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM
OS 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum).
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanothermobacter.
OX NCBI_TaxID=187420;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-13, AND FUNCTION.
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=9851985; DOI=10.1128/jb.180.24.6446-6449.1998;
RA Kim H.-S., Vothknecht U.C., Hedderich R., Celic I., Soell D.;
RT "Sequence divergence of seryl-tRNA synthetases in archaea.";
RL J. Bacteriol. 180:6446-6449(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=9371463; DOI=10.1128/jb.179.22.7135-7155.1997;
RA Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J.,
RA Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D.,
RA Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R.,
RA Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D.,
RA Safer H., Patwell D., Prabhakar S., McDougall S., Shimer G., Goyal A.,
RA Pietrovski S., Church G.M., Daniels C.J., Mao J.-I., Rice P., Noelling J.,
RA Reeve J.N.;
RT "Complete genome sequence of Methanobacterium thermoautotrophicum deltaH:
RT functional analysis and comparative genomics.";
RL J. Bacteriol. 179:7135-7155(1997).
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:0000269|PubMed:9851985}.
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 -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
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:0000250};
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. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
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:0000250}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type-2 seryl-tRNA synthetase subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF009823; AAB87409.1; -; Genomic_DNA.
DR EMBL; AE000666; AAB85611.1; -; Genomic_DNA.
DR PIR; D69016; D69016.
DR RefSeq; WP_010876746.1; NC_000916.1.
DR AlphaFoldDB; O27194; -.
DR SMR; O27194; -.
DR STRING; 187420.MTH_1122; -.
DR PRIDE; O27194; -.
DR EnsemblBacteria; AAB85611; AAB85611; MTH_1122.
DR GeneID; 1471530; -.
DR KEGG; mth:MTH_1122; -.
DR PATRIC; fig|187420.15.peg.1099; -.
DR HOGENOM; CLU_542524_0_0_2; -.
DR OMA; YYVCPPK; -.
DR UniPathway; UPA00906; UER00895.
DR Proteomes; UP000005223; 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; IPR002314; aa-tRNA-synt_IIb.
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; PF00587; tRNA-synt_2b; 1.
DR Pfam; PF18490; tRNA_bind_4; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00415; serS_MJ; 1.
PE 1: Evidence at protein level;
KW Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Direct protein sequencing; Ligase; Metal-binding; Nucleotide-binding;
KW Protein biosynthesis; Reference proteome; Zinc.
FT CHAIN 1..513
FT /note="Type-2 serine--tRNA ligase"
FT /id="PRO_0000122177"
FT BINDING 312
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 314
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 344..346
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 344
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 355..356
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 361..363
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 363
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 467
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 474
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT CONFLICT 150
FT /note="F -> V (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
FT CONFLICT 187
FT /note="D -> E (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
FT CONFLICT 230
FT /note="F -> L (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
FT CONFLICT 242
FT /note="E -> R (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
FT CONFLICT 358
FT /note="E -> D (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
FT CONFLICT 501
FT /note="V -> VV (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
FT CONFLICT 503..504
FT /note="NP -> KG (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
FT CONFLICT 513
FT /note="D -> T (in Ref. 2; AAB87409)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 513 AA; 58808 MW; 213B65D10773AA2A CRC64;
MKFKLKGIIK LSKEVPGIED DLEKFFTEAE SDILRRGVPE GQEHEAAHIK SWRLEGDTLH
IEMESGRRVR AHDGLLRLKK PLGQLLGPKY RVGVRGISVT DYTMEMKAPG VSGIPSLAEL
PFVEDAAITD GTIMVRFQPL EESDLRKHVF DRVVKHARTL VESSDDLTVQ VTRATPGEII
ARSRSRDFFF EGDPTEEAMR LGWVKKFPGR GQWFYGPKIT ALHRALEEFF IERIVKPLGF
VECLFPKLIP LDIMNKMRYL EGLPEGMYYC SAPSRDPETF EEFKNELIIN REVPMDLLKR
GIKDPGYVIA PAQCEPFYQF LSHEVVSAED LPVKFFDRSG WTYRWEAGGS KGLDRVHEFQ
RVELVWLAEP GETEEIRDRT VELSHDAADE LELEWYTEVG DDPFYLEGRK VEERGIEFPD
VPKYEMRLSL PGREKGVAVV SANVHGTHFI EGFSIREARN LNIWTGCTGI GLSRWIYGFL
AQKGFETGNW PDFIGERVEG VENPRIITWP RQD
