SYS2_METKA
ID SYS2_METKA Reviewed; 527 AA.
AC Q8TVD2;
DT 01-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 104.
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=MK1460;
OS Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938).
OC Archaea; Euryarchaeota; Methanopyri; Methanopyrales; Methanopyraceae;
OC Methanopyrus.
OX NCBI_TaxID=190192;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AV19 / DSM 6324 / JCM 9639 / NBRC 100938;
RX PubMed=11930014; DOI=10.1073/pnas.032671499;
RA Slesarev A.I., Mezhevaya K.V., Makarova K.S., Polushin N.N.,
RA Shcherbinina O.V., Shakhova V.V., Belova G.I., Aravind L., Natale D.A.,
RA Rogozin I.B., Tatusov R.L., Wolf Y.I., Stetter K.O., Malykh A.G.,
RA Koonin E.V., Kozyavkin S.A.;
RT "The complete genome of hyperthermophile Methanopyrus kandleri AV19 and
RT monophyly of archaeal methanogens.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:4644-4649(2002).
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; AE009439; AAM02673.1; -; Genomic_DNA.
DR PDB; 3W3S; X-ray; 3.10 A; A=1-527.
DR PDBsum; 3W3S; -.
DR AlphaFoldDB; Q8TVD2; -.
DR SMR; Q8TVD2; -.
DR STRING; 190192.MK1460; -.
DR PRIDE; Q8TVD2; -.
DR EnsemblBacteria; AAM02673; AAM02673; MK1460.
DR KEGG; mka:MK1460; -.
DR PATRIC; fig|190192.8.peg.1616; -.
DR HOGENOM; CLU_542524_0_0_2; -.
DR OMA; YYVCPPK; -.
DR BRENDA; 6.1.1.11; 3274.
DR UniPathway; UPA00906; UER00895.
DR Proteomes; UP000001826; 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; 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; PF00587; tRNA-synt_2b; 1.
DR Pfam; PF18490; tRNA_bind_4; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00415; serS_MJ; 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 Metal-binding; Nucleotide-binding; Protein biosynthesis;
KW Reference proteome; Zinc.
FT CHAIN 1..527
FT /note="Type-2 serine--tRNA ligase"
FT /id="PRO_0000286169"
FT BINDING 317
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 319
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 349..351
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 349
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 360..361
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 366..368
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 368
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 478
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT BINDING 485
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01278"
FT STRAND 2..15
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 19..35
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 58..71
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 73..92
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 96..109
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 126..130
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 132..141
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 144..148
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 151..163
FT /evidence="ECO:0007829|PDB:3W3S"
FT TURN 164..167
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 196..202
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 215..217
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 219..235
FT /evidence="ECO:0007829|PDB:3W3S"
FT TURN 236..241
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 253..258
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 261..264
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 266..268
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 279..292
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 297..305
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 312..314
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 321..326
FT /evidence="ECO:0007829|PDB:3W3S"
FT TURN 333..335
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 338..342
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 345..348
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 358..360
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 362..373
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 375..395
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 400..404
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 412..414
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 415..418
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 428..434
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 436..438
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 444..446
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 447..457
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 459..463
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 467..470
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 475..482
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 483..494
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 498..500
FT /evidence="ECO:0007829|PDB:3W3S"
FT HELIX 503..513
FT /evidence="ECO:0007829|PDB:3W3S"
FT STRAND 523..525
FT /evidence="ECO:0007829|PDB:3W3S"
SQ SEQUENCE 527 AA; 61368 MW; 7526147D81EFC5CD CRC64;
MELKFSAEVE LTLSREVDPA EIEPTVEEFV KEANEDLLQR GVPTGKEGAK IESYRVLEDT
IEMEITGTRY LRPHEAAMRV RKRLAERLGR KHRVGVRDLK IPRYEVVLRF DREVTRDDVG
YVPVADDVVV EDGTVRLTFQ DVDEEMLRRH VIDRVIRLVA WAVEERSELV ERVTKVEPGT
VVDESGPREI RFDGDVTEEA RRRGWVKEFP GRGQWIYTPP MAALFEVLRD FLLERVTRKL
GFEPALFPKL IPLETMFRMR YLHGLPDGMY YVCPPKRDPE LFDDFKRELY VWGELNERTL
GSLKEKLRDP GYVLAPAQCE PFYELLRDEV VDPERLPIKL YDCSGWTYRW EGGAAKGLER
VNEFQRIEHV WIAEPEEAER IREELLEATK RVAEELELEW KVVVSDDPFY LEGRLLEDRD
IELPDVPSYE FEVYLPFKGE RSSEEAWISV GSFNVHGEHF VDGFNVKEKS GRTLFTGCAG
LGVTRWVVGL LAQHGFEPEE WPEPILERID EKFGGLPEVP KTLTWPE
