SYS2_METBF
ID SYS2_METBF Reviewed; 502 AA.
AC Q46AN5;
DT 01-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2005, sequence version 1.
DT 03-AUG-2022, entry version 111.
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=serS2; OrderedLocusNames=Mbar_A2126;
OS Methanosarcina barkeri (strain Fusaro / DSM 804).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=269797;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Fusaro / DSM 804;
RX PubMed=16980466; DOI=10.1128/jb.00810-06;
RA Maeder D.L., Anderson I., Brettin T.S., Bruce D.C., Gilna P., Han C.S.,
RA Lapidus A., Metcalf W.W., Saunders E., Tapia R., Sowers K.R.;
RT "The Methanosarcina barkeri genome: comparative analysis with
RT Methanosarcina acetivorans and Methanosarcina mazei reveals extensive
RT rearrangement within methanosarcinal genomes.";
RL J. Bacteriol. 188:7922-7931(2006).
RN [2]
RP FUNCTION, KINETIC PARAMETERS, AND TRNA(SER) RECOGNITION.
RX PubMed=15364939; DOI=10.1074/jbc.m408753200;
RA Korencic D., Polycarpo C., Weygand-Durasevic I., Soell D.;
RT "Differential modes of transfer RNA(Ser) recognition in Methanosarcina
RT barkeri.";
RL J. Biol. Chem. 279:48780-48786(2004).
RN [3]
RP ACTIVITY REGULATION.
RX PubMed=16054140; DOI=10.1016/j.febslet.2005.06.073;
RA Ahel D., Slade D., Mocibob M., Soell D., Weygand-Durasevic I.;
RT "Selective inhibition of divergent seryl-tRNA synthetases by serine
RT analogues.";
RL FEBS Lett. 579:4344-4348(2005).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH ZINC; ATP;
RP SUBSTRATE AND SUBSTRATE ANALOG, COFACTOR, SUBUNIT, MUTAGENESIS OF CYS-306;
RP GLU-355 AND CYS-461, AND SERINE RECOGNITION MECHANISM.
RX PubMed=16675947; DOI=10.1038/sj.emboj.7601129;
RA Bilokapic S., Maier T., Ahel D., Gruic-Sovulj I., Soell D.,
RA Weygand-Durasevic I., Ban N.;
RT "Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-
RT dependent mode of substrate recognition.";
RL EMBO J. 25:2498-2509(2006).
CC -!- FUNCTION: Catalyzes the attachment of serine to tRNA(Ser). Is also
CC probably able to aminoacylate tRNA(Sec) with serine, to form the
CC misacylated tRNA L-seryl-tRNA(Sec), which will be further converted
CC into selenocysteinyl-tRNA(Sec). {ECO:0000269|PubMed:15364939}.
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;
CC Evidence={ECO:0000269|PubMed:16675947};
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.
CC {ECO:0000269|PubMed:16675947};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16675947};
CC Note=Binds 2 magnesium ions per subunit. One ion coordinates the alpha
CC and beta phosphates of ATP, and the other coordinates the beta and
CC gamma phosphates. {ECO:0000269|PubMed:16675947};
CC -!- ACTIVITY REGULATION: Inhibited by serinamide, unlike type-1 M.barkeri
CC SerRS. {ECO:0000269|PubMed:16054140}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=25 uM for L-serine {ECO:0000269|PubMed:15364939};
CC KM=13.6 uM for ATP {ECO:0000269|PubMed:15364939};
CC KM=3 uM for tRNA(Ser CGA) {ECO:0000269|PubMed:15364939};
CC KM=4.7 uM for tRNA(Ser GGA) {ECO:0000269|PubMed:15364939};
CC KM=5.3 uM for tRNA(Ser GCU) {ECO:0000269|PubMed:15364939};
CC Note=Catalytic efficiency is similar with the tRNA(Ser CGA) and
CC tRNA(Ser GGA) isoacceptors, but is 5-fold lower with tRNA(Ser GCU).;
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:16675947}.
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 -!- 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; CP000099; AAZ71057.1; -; Genomic_DNA.
DR RefSeq; WP_011307103.1; NC_007355.1.
DR PDB; 2CIM; X-ray; 2.51 A; A/B=1-502.
DR PDB; 2CJ9; X-ray; 2.30 A; A/B=1-502.
DR PDB; 2CJA; X-ray; 2.20 A; A/B=1-502.
DR PDB; 2CJB; X-ray; 2.70 A; A/B=1-502.
DR PDBsum; 2CIM; -.
DR PDBsum; 2CJ9; -.
DR PDBsum; 2CJA; -.
DR PDBsum; 2CJB; -.
DR AlphaFoldDB; Q46AN5; -.
DR SMR; Q46AN5; -.
DR STRING; 269797.Mbar_A2126; -.
DR EnsemblBacteria; AAZ71057; AAZ71057; Mbar_A2126.
DR GeneID; 3626080; -.
DR KEGG; mba:Mbar_A2126; -.
DR eggNOG; arCOG00403; Archaea.
DR HOGENOM; CLU_542524_0_0_2; -.
DR OMA; YYVCPPK; -.
DR OrthoDB; 9543at2157; -.
DR UniPathway; UPA00906; UER00895.
DR EvolutionaryTrace; Q46AN5; -.
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; IPR006195; aa-tRNA-synth_II.
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.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Magnesium; Metal-binding; Nucleotide-binding; Protein biosynthesis; Zinc.
FT CHAIN 1..502
FT /note="Type-2 serine--tRNA ligase"
FT /id="PRO_0000285289"
FT BINDING 304
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT BINDING 306
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 336..338
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 336
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT BINDING 336
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 338
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 347..348
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 353..355
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT BINDING 355
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 400
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT BINDING 416
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 432
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 432
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 435
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT BINDING 435
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT BINDING 461
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 468
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT MUTAGEN 306
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16675947"
FT MUTAGEN 355
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16675947"
FT MUTAGEN 461
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16675947"
FT STRAND 4..15
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 18..20
FT /evidence="ECO:0007829|PDB:2CIM"
FT HELIX 22..31
FT /evidence="ECO:0007829|PDB:2CJA"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 35..37
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 47..51
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 58..64
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 66..68
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 70..84
FT /evidence="ECO:0007829|PDB:2CJA"
FT TURN 86..88
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 95..106
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 126..133
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 137..141
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 144..160
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 170..173
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 185..191
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 194..197
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 204..206
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 208..224
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 226..229
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 242..248
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 250..252
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 255..257
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 269..282
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 287..293
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 299..301
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 303..306
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 307..312
FT /evidence="ECO:0007829|PDB:2CJA"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 320..322
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 324..329
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 331..335
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 349..361
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 362..382
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 388..393
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 396..400
FT /evidence="ECO:0007829|PDB:2CJ9"
FT STRAND 408..411
FT /evidence="ECO:0007829|PDB:2CJ9"
FT STRAND 413..419
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 422..424
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 431..438
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 442..447
FT /evidence="ECO:0007829|PDB:2CJA"
FT STRAND 457..465
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 466..477
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 481..483
FT /evidence="ECO:0007829|PDB:2CJA"
FT HELIX 486..492
FT /evidence="ECO:0007829|PDB:2CJA"
SQ SEQUENCE 502 AA; 57828 MW; C1A6D21716C69A5A CRC64;
MKLQFNLKAY FKTSADPTPA KDAIAALFEE ANSTLLTRGA PEGQGAKVTE WKLGEDRIEL
TLQSGRYVRV HDAIFRLRKQ LAEALGKKYK IGIRGIEVES FIIKVPADHE LRMLKVPYIK
SMENIEGGIQ LELEVGEAEM KNRVPDRILT LLEEKIEAAQ YGAKAEHWNL LWQREPMEHP
FKEDPTQAMM KEGWLKRGSS RGQWIHGPQS ARIFRTFEKI VLEELLEPLG YREMIFPKLV
TWEVWMKSGH AKGVYPEIYY VCPPQTRDPD YWEEVADYYK VTHEVPTKLI KEKIAEPIGG
MCYAQCPPFW MYVAGETLPN EEIPVKVFDR SGTSHRYESG GIHGIERVDE FHRIEIVWIG
TKEEVLKCAE ELHDRYMHIF NDILDIEWRK ARVTPWFMAQ EGLLGLAEEN TVGTTDYEAC
LPYRGPDGEW LEFQNVSING DKYPKGFNVK LQSGDELWSG CSGVGLERWA AVFLAQKGLD
PANWPEEFRN RVGEMPKGIR FL
