ID A0A1Y4GHG9_9ACTN Unreviewed; 676 AA.
AC A0A1Y4GHG9;
DT 30-AUG-2017, integrated into UniProtKB/TrEMBL.
DT 30-AUG-2017, sequence version 1.
DT 27-MAR-2024, entry version 32.
DE RecName: Full=Lysine--tRNA ligase {ECO:0000256|HAMAP-Rule:MF_00252};
DE EC=6.1.1.6 {ECO:0000256|HAMAP-Rule:MF_00252};
DE AltName: Full=Lysyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00252};
DE Short=LysRS {ECO:0000256|HAMAP-Rule:MF_00252};
GN Name=lysS {ECO:0000256|HAMAP-Rule:MF_00252};
GN ORFNames=B5F40_02240 {ECO:0000313|EMBL:OUO91681.1};
OS Gordonibacter sp. An230.
OC Bacteria; Actinomycetota; Coriobacteriia; Eggerthellales; Eggerthellaceae;
OC Gordonibacter.
OX NCBI_TaxID=1965592 {ECO:0000313|EMBL:OUO91681.1, ECO:0000313|Proteomes:UP000196177};
RN [1] {ECO:0000313|Proteomes:UP000196177}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=An230 {ECO:0000313|Proteomes:UP000196177};
RA Medvecky M., Cejkova D., Polansky O., Karasova D., Kubasova T., Cizek A.,
RA Rychlik I.;
RT "Function of individual gut microbiota members based on whole genome
RT sequencing of pure cultures obtained from chicken caecum.";
RL Submitted (APR-2017) to the EMBL/GenBank/DDBJ databases.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-
CC tRNA(Lys); Xref=Rhea:RHEA:20792, Rhea:RHEA-COMP:9696, Rhea:RHEA-
CC COMP:9697, ChEBI:CHEBI:30616, ChEBI:CHEBI:32551, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78529, ChEBI:CHEBI:456215; EC=6.1.1.6;
CC Evidence={ECO:0000256|ARBA:ARBA00000204, ECO:0000256|HAMAP-
CC Rule:MF_00252, ECO:0000256|RuleBase:RU000336};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00252,
CC ECO:0000256|RuleBase:RU000336};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000256|HAMAP-Rule:MF_00252,
CC ECO:0000256|RuleBase:RU000336};
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00252}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00252}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000256|HAMAP-Rule:MF_00252}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:OUO91681.1}.
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DR EMBL; NFJP01000003; OUO91681.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1Y4GHG9; -.
DR OrthoDB; 9801152at2; -.
DR Proteomes; UP000196177; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004824; F:lysine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004825; F:methionine-tRNA ligase activity; IEA:InterPro.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR GO; GO:0006431; P:methionyl-tRNA aminoacylation; IEA:InterPro.
DR CDD; cd00775; LysRS_core; 1.
DR CDD; cd04322; LysRS_N; 1.
DR CDD; cd02800; tRNA_bind_EcMetRS_like; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 2.
DR HAMAP; MF_00252; Lys_tRNA_synth_class2; 1.
DR InterPro; IPR004364; Aa-tRNA-synt_II.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR002313; Lys-tRNA-ligase_II.
DR InterPro; IPR044136; Lys-tRNA-ligase_II_N.
DR InterPro; IPR018149; Lys-tRNA-synth_II_C.
DR InterPro; IPR004495; Met-tRNA-synth_bsu_C.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004365; NA-bd_OB_tRNA.
DR InterPro; IPR002547; tRNA-bd_dom.
DR NCBIfam; TIGR00499; lysS_bact; 1.
DR PANTHER; PTHR42918:SF9; LYSINE--TRNA LIGASE; 1.
DR PANTHER; PTHR42918; LYSYL-TRNA SYNTHETASE; 1.
DR Pfam; PF00152; tRNA-synt_2; 1.
DR Pfam; PF01336; tRNA_anti-codon; 1.
DR Pfam; PF01588; tRNA_bind; 1.
DR PRINTS; PR00982; TRNASYNTHLYS.
DR SUPFAM; SSF55681; Class II aaRS and biotin synthetases; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 2.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
DR PROSITE; PS50886; TRBD; 1.
PE 3: Inferred from homology;
KW Aminoacyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00252};
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00252};
KW Ligase {ECO:0000256|HAMAP-Rule:MF_00252, ECO:0000313|EMBL:OUO91681.1};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00252, ECO:0000256|RuleBase:RU000336};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00252,
KW ECO:0000256|RuleBase:RU000336};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Protein biosynthesis {ECO:0000256|HAMAP-Rule:MF_00252};
KW RNA-binding {ECO:0000256|ARBA:ARBA00022884, ECO:0000256|PROSITE-
KW ProRule:PRU00209};
KW tRNA-binding {ECO:0000256|ARBA:ARBA00022555, ECO:0000256|PROSITE-
KW ProRule:PRU00209}.
FT DOMAIN 185..494
FT /note="Aminoacyl-transfer RNA synthetases class-II family
FT profile"
FT /evidence="ECO:0000259|PROSITE:PS50862"
FT DOMAIN 571..676
FT /note="TRNA-binding"
FT /evidence="ECO:0000259|PROSITE:PS50886"
FT REGION 501..540
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 518..535
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 410
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 417
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 417
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
SQ SEQUENCE 676 AA; 75270 MW; C4D127B6DA782E45 CRC64;
MSETPDQTQQ IIEDDPIAVR RAKREALIAA GKDPYGHAFK HSHHLAELNE RYADLEDGAS
TEDEVQVAGR VMAKRDQGKL AFLELRDSSG DMQLFCRVNA LGEEAYRQLK DLDVGDWIGV
RGTMMRTKRG QLSVAVASFE LLSKSLRPLP EKFHGLADKE TRYRQRYVDL VMNPEVKQVF
EKRFKIVAAI RRYMEEQGFY EVETPFLHPI LGGANAKPFV THFNALDRDY YLRIATELPL
KRLLVGGFEK VFEIGRQFRN EGMDPYHNPE FTTMEAYQAF SDLEGMMELT QGYIQAAAMA
ACGTLQITYQ GQEVDLSGEW PRKSMIELAS AGAGEDVSFA RTRDELAAIL EKNGGHADSA
WGKGKLIAEI FEAVAEEKLI QPTFVIDHPL EVSPLAKKKA GDPNLTERFE LFICGHEYAN
AFGELNDPVD QAERFRAQVE AKDMGDDEAM GYDEDYVRAL EYGMPPAGGV GVGIDRLVML
LADAPSIRDV LLFPHMRDEQ HAPARAGSMS SSSPLDRSIP HMRDETPDGG RERAAEAAAD
AAASDAPAPA AFDFSKVVIE PLFEEQVDFE TFSKSDFRAV KVKECVAVPK SKKLLKFTLD
DGTDADRIIL SGIHAYYEPE DLLGKTLVAI TNLPPRKMMG IDSCGMIISA VHEEEGEERL
NLLMVDDRIP AGAKLY
//
