ID SYS2_METVS Reviewed; 514 AA.
AC A6UN84;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 21-AUG-2007, sequence version 1.
DT 27-MAR-2024, entry version 73.
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=Mevan_0041;
OS Methanococcus vannielii (strain ATCC 35089 / DSM 1224 / JCM 13029 / OCM 148
OS / SB).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanococcaceae; Methanococcus.
OX NCBI_TaxID=406327;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35089 / DSM 1224 / JCM 13029 / OCM 148 / SB;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Anderson I.,
RA Sieprawska-Lupa M., Whitman W.B., Richardson P.;
RT "Complete sequence of Methanococcus vannielii SB.";
RL Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000742; ABR53956.1; -; Genomic_DNA.
DR RefSeq; WP_011971860.1; NC_009634.1.
DR AlphaFoldDB; A6UN84; -.
DR SMR; A6UN84; -.
DR STRING; 406327.Mevan_0041; -.
DR GeneID; 5325630; -.
DR KEGG; mvn:Mevan_0041; -.
DR eggNOG; arCOG00403; Archaea.
DR HOGENOM; CLU_542524_0_0_2; -.
DR OrthoDB; 115981at2157; -.
DR UniPathway; UPA00906; UER00895.
DR Proteomes; UP000001107; 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:0006434; P:seryl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd00670; Gly_His_Pro_Ser_Thr_tRS_core; 1.
DR Gene3D; 3.30.70.1920; -; 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 NCBIfam; TIGR00415; serS_MJ; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR Pfam; PF18490; tRNA_bind_4; 1.
DR SUPFAM; SSF55681; Class II aaRS and biotin synthetases; 1.
PE 3: Inferred from homology;
KW Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase; Metal-binding;
KW Nucleotide-binding; Protein biosynthesis; Zinc.
FT CHAIN 1..514
FT /note="Type-2 serine--tRNA ligase"
FT /id="PRO_1000165224"
FT BINDING 313
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 315
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 344..346
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 344
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 355..356
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 361..363
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 363
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 470
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 477
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
SQ SEQUENCE 514 AA; 59899 MW; 4B1D5EE11E525CA5 CRC64;
MRFELDGRII FSKDVTKEAQ IEILEVLENR DIFLKGVPEG KEGDASKIES YKFEGKDLVL
KMTSGTYTRA HEGIVRLKKP IMEKIGRNHQ IGIRDVTIDK YVITIDSEIS KVEQLKGLKV
PECELKLEGE KINIIFKNVG DGELKRNIID RAIKFVKNEL DKQDQDLTYE VCKIAPGTIV
SEYQAQRKTG FFSDPTDLAE SLGWVKKFPG RGQWFYTPPM AKLFRAFENL IIEECIQKIE
FDECLFPKLI PLDVMYKMRY LEGLPEGMYY VCPPKREPEM FQDFVNEMMI KKEIPIDKLK
ELLRDPAYVL APAQCEPFYT LFDHELVDID SPVKFFDKSG WTYRWEGGGA KGLDRVNEFL
RSECVWMGSP KFVEEVRDDT LKYAEDLAKK LDLEYWTEVG DDPFYLEGRK KDDRSIEFPD
VPKYEMRLWL PHIKEERKGV AVTSANIHGT HFVEGFGIKD YKDRKVWTGC TGFGLTRWII
GFLAQYGFEY SDWPDMIKDK VLEMPKIPKM ITWP
//
