SYS2_METMP
ID SYS2_METMP Reviewed; 514 AA.
AC O30520;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 13-APR-2004, sequence version 2.
DT 03-AUG-2022, entry version 118.
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=MMP0879;
OS Methanococcus maripaludis (strain S2 / LL).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanococcaceae; Methanococcus.
OX NCBI_TaxID=267377;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
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=S2 / LL;
RX PubMed=15466049; DOI=10.1128/jb.186.20.6956-6969.2004;
RA Hendrickson E.L., Kaul R., Zhou Y., Bovee D., Chapman P., Chung J.,
RA Conway de Macario E., Dodsworth J.A., Gillett W., Graham D.E., Hackett M.,
RA Haydock A.K., Kang A., Land M.L., Levy R., Lie T.J., Major T.A.,
RA Moore B.C., Porat I., Palmeiri A., Rouse G., Saenphimmachak C., Soell D.,
RA Van Dien S., Wang T., Whitman W.B., Xia Q., Zhang Y., Larimer F.W.,
RA Olson M.V., Leigh J.A.;
RT "Complete genome sequence of the genetically tractable hydrogenotrophic
RT methanogen Methanococcus maripaludis.";
RL J. Bacteriol. 186:6956-6969(2004).
RN [3]
RP FUNCTION, AND SUBUNIT.
RX PubMed=14764085; DOI=10.1111/j.1432-1033.2003.03971.x;
RA Bilokapic S., Korencic D., Soell D., Weygand-Durasevic I.;
RT "The unusual methanogenic seryl-tRNA synthetase recognizes tRNASer species
RT from all three kingdoms of life.";
RL Eur. J. Biochem. 271:694-702(2004).
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:14764085, 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:0000269|PubMed:14764085}.
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}.
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DR EMBL; AF009822; AAD03476.1; -; Genomic_DNA.
DR EMBL; BX950229; CAF30435.1; -; Genomic_DNA.
DR RefSeq; WP_011170823.1; NC_005791.1.
DR AlphaFoldDB; O30520; -.
DR SMR; O30520; -.
DR STRING; 267377.MMP0879; -.
DR EnsemblBacteria; CAF30435; CAF30435; MMP0879.
DR GeneID; 2762696; -.
DR KEGG; mmp:MMP0879; -.
DR PATRIC; fig|267377.15.peg.905; -.
DR eggNOG; arCOG00403; Archaea.
DR HOGENOM; CLU_542524_0_0_2; -.
DR OMA; YYVCPPK; -.
DR OrthoDB; 9543at2157; -.
DR BioCyc; MetaCyc:MON-14955; -.
DR BioCyc; MMAR267377:MMP_RS04570-MON; -.
DR UniPathway; UPA00906; UER00895.
DR Proteomes; UP000000590; 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; Ligase; Metal-binding;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome; Zinc.
FT CHAIN 1..514
FT /note="Type-2 serine--tRNA ligase"
FT /id="PRO_0000122176"
FT BINDING 313
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 315
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 470
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 477
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT CONFLICT 16
FT /note="S -> E (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 54
FT /note="E -> Q (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 100
FT /note="T -> S (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 129
FT /note="N -> G (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 169
FT /note="F -> K (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 186
FT /note="T -> K (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 239
FT /note="V -> I (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 282
FT /note="R -> K (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
FT CONFLICT 297
FT /note="D -> E (in Ref. 1; AAD03476)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 514 AA; 59587 MW; 75141EDFA3CFD878 CRC64;
MRFELEGRII FSKDVSEETQ KDIIEVLENG DIFLKGVPEG KENEASKIEG YEFEGKDLKL
NMTSGTYTRA HEGIVRLKKP IMEKVGRKHQ IGIRDVAIDT YVVTITATPS KVAELKGLKV
PECEVELDNE KIKILFKNLG DGELKRNIID RAIKFVKTEL DKQEQDLTFE VCKIAPGTIV
SDYKATREIT FDKDPTELAE PYGWVKRFPG RGQWFYTAPM AKLFRAFESL IVEECIEKVG
FDECLFPKLI PLDVMYKMRY LEGLPEGMYY VCPPKREPEM FRDFVNEMMI KKEIPIDKLK
TLLRDPGYVL APAQCEPFYT FFDHELVDVD SPSKFFDKSG WTYRWEGGGA KGLDRVNEFL
RGECVWMGSP EFVEKVRDDT LKYAEKLAEK LDLEYWTEVG DDPFYLEGRK NEDRGIEFPD
VPKYEMRLWL PHVKDERKGV AVTSANIHGT HFVEGFGIKD YKDRKVWTGC TGYGLSRWLI
GFLAQYGYNY EDWPEIIQKK VGKLPEIPKL ITWP
