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SYS2_METVS
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   03-AUG-2022, entry version 67.
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   EnsemblBacteria; ABR53956; ABR53956; Mevan_0041.
DR   GeneID; 5325630; -.
DR   KEGG; mvn:Mevan_0041; -.
DR   eggNOG; arCOG00403; Archaea.
DR   HOGENOM; CLU_542524_0_0_2; -.
DR   OMA; YYVCPPK; -.
DR   OrthoDB; 9543at2157; -.
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: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   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
 
 
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