ID M0QKW4_9ACTN Unreviewed; 1146 AA.
AC M0QKW4;
DT 03-APR-2013, integrated into UniProtKB/TrEMBL.
DT 03-APR-2013, sequence version 1.
DT 27-MAR-2024, entry version 60.
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 ECO:0000313|EMBL:GAC69285.1};
GN ORFNames=GS4_23_00820 {ECO:0000313|EMBL:GAC69285.1};
OS Gordonia soli NBRC 108243.
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Gordoniaceae;
OC Gordonia.
OX NCBI_TaxID=1223545 {ECO:0000313|EMBL:GAC69285.1, ECO:0000313|Proteomes:UP000011666};
RN [1] {ECO:0000313|EMBL:GAC69285.1, ECO:0000313|Proteomes:UP000011666}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 108243 {ECO:0000313|EMBL:GAC69285.1,
RC ECO:0000313|Proteomes:UP000011666};
RA Isaki-Nakamura S., Hosoyama A., Tsuchikane K., Ando Y., Baba S., Ohji S.,
RA Hamada M., Tamura T., Yamazoe A., Yamazaki S., Fujita N.;
RT "Whole genome shotgun sequence of Gordonia soli NBRC 108243.";
RL Submitted (JAN-2013) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the production of L-lysyl-tRNA(Lys)transfer and the
CC transfer of a lysyl group from L-lysyl-tRNA(Lys) to membrane-bound
CC phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol
CC (LPG), one of the components of the bacterial membrane with a positive
CC net charge. LPG synthesis contributes to the resistance to cationic
CC antimicrobial peptides (CAMPs) and likely protects M.tuberculosis
CC against the CAMPs produced by competiting microorganisms
CC (bacteriocins). In fact, the modification of anionic
CC phosphatidylglycerol with positively charged L-lysine results in
CC repulsion of the peptides. {ECO:0000256|ARBA:ARBA00024681}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + L-lysyl-
CC tRNA(Lys) = 1,2-diacyl-sn-glycero-3-phospho-1'-(3'-O-L-lysyl)-sn-
CC glycerol + tRNA(Lys); Xref=Rhea:RHEA:10668, Rhea:RHEA-COMP:9696,
CC Rhea:RHEA-COMP:9697, ChEBI:CHEBI:64716, ChEBI:CHEBI:75792,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78529; EC=2.3.2.3;
CC Evidence={ECO:0000256|ARBA:ARBA00000367};
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};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00252};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_00252};
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00252}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004651};
CC Multi-pass membrane protein {ECO:0000256|ARBA:ARBA00004651}. Cytoplasm
CC {ECO:0000256|HAMAP-Rule:MF_00252}. Membrane
CC {ECO:0000256|ARBA:ARBA00004141}; Multi-pass membrane protein
CC {ECO:0000256|ARBA:ARBA00004141}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000256|HAMAP-Rule:MF_00252}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the class-II
CC aminoacyl-tRNA synthetase family. {ECO:0000256|ARBA:ARBA00009968}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the LPG synthetase
CC family. {ECO:0000256|ARBA:ARBA00005270}.
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:GAC69285.1}.
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DR EMBL; BANX01000023; GAC69285.1; -; Genomic_DNA.
DR RefSeq; WP_007622198.1; NZ_BANX01000023.1.
DR AlphaFoldDB; M0QKW4; -.
DR STRING; 1223545.GS4_23_00820; -.
DR eggNOG; COG1190; Bacteria.
DR eggNOG; COG2898; Bacteria.
DR OrthoDB; 9801152at2; -.
DR Proteomes; UP000011666; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; 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:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0050071; F:phosphatidylglycerol lysyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0006629; P:lipid metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR CDD; cd04322; LysRS_N; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
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; IPR024320; LPG_synthase_C.
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; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004365; NA-bd_OB_tRNA.
DR InterPro; IPR031553; tRNA-synt_2_TM.
DR NCBIfam; TIGR00499; lysS_bact; 1.
DR PANTHER; PTHR42918:SF9; LYSINE--TRNA LIGASE; 1.
DR PANTHER; PTHR42918; LYSYL-TRNA SYNTHETASE; 1.
DR Pfam; PF09924; LPG_synthase_C; 1.
DR Pfam; PF00152; tRNA-synt_2; 1.
DR Pfam; PF16995; tRNA-synt_2_TM; 1.
DR Pfam; PF01336; tRNA_anti-codon; 1.
DR PRINTS; PR00982; TRNASYNTHLYS.
DR SUPFAM; SSF55681; Class II aaRS and biotin synthetases; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 3: Inferred from homology;
KW Aminoacyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00252};
KW Antibiotic resistance {ECO:0000256|ARBA:ARBA00023251};
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Cell membrane {ECO:0000256|ARBA:ARBA00022475};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00252};
KW Ligase {ECO:0000256|HAMAP-Rule:MF_00252, ECO:0000313|EMBL:GAC69285.1};
KW Lipid metabolism {ECO:0000256|ARBA:ARBA00023098};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00252};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|SAM:Phobius};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Protein biosynthesis {ECO:0000256|HAMAP-Rule:MF_00252};
KW Reference proteome {ECO:0000313|Proteomes:UP000011666};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692, ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989,
KW ECO:0000256|SAM:Phobius}.
FT TRANSMEM 62..83
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 98..119
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 126..146
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 161..181
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 193..218
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 823..1142
FT /note="Aminoacyl-transfer RNA synthetases class-II family
FT profile"
FT /evidence="ECO:0000259|PROSITE:PS50862"
FT REGION 1..32
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 9..23
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 1055
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 1062
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 1062
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
SQ SEQUENCE 1146 AA; 126566 MW; DBE5858859D2A260 CRC64;
MTVDIDDGVQ HSGDGHPRGR HPGGVDPAEL PARERTAADR RSLALLERIR SPRGFGRNGP
RIAGTVVGIL AAISLLSSVF PFFRHAIHYP RDYVDDYIIT MPDTSFAWAF VLALIAVALS
ARKRIAWWIC LVYLLLFMIT AVVYLLPPVA REYGVDDVQR LNIIIGLAID LVAVVFLIAS
YRQFYTRVRR GAVFAALAVL VGGLVVGTVV GWGLVWLFPH TLTRAERLPY AINRVVAFAA
VDQDNFNGHH TFPPINGLLG LFGALALMAA AIVLFRSLRL RSLMTAEDER LIRALIARFN
DDDSLAYFST RRDKAVVFSP DGRAAVTYRV EVGVGIAGGD PIGDPDSWPD AIAEFLALCE
RYGWHPAAMG PSARGAQAYD AAGFGSLNIG DEAILRTRDY SLNGPAMKGV RHAVTRARRA
GISVRIRRHL ELSAEEMAEV VARADAWRDT DEERGFAMAL SRVGDPSDGD CLLVEAVENA
DTPDEKVVGM LSFVPWGRTG VSLDLMRRDR NSVNGIVETM VTELARNSET VGITEVSLNF
AAFRAFFENG PQIGAGPVMR LTYSVLMFGS RFFQMESLYK SNAKYLPDWE PRFLCFEDNR
MIPRVGLAAI VTEGFVRLPT FGRKRHYTDG TPAIPAGVDV DQLIAELDTE RRDADSVDVH
RPEQVRVRIA KMDRLIAEGI DPYPPADPPT HTIAEAAAAP QGTGVRISGR ITRLRDFGKV
VFADVHDWSG QIQVLIDASK LVEGTPDFAG DVDLGDLVEV TGEVGTSRKG ELSVVMLTWR
MLGKCLHPLP DKWSGLTDPE ARVRQRYVDL AINKESRDLL ATRSVVVKSL RDFLSARGYL
EVETPILQQI HGGANATPFQ THINAYDLDL YLRIAPELYL KRLCVGGVEK VFEIGRNFRN
EGVDFSHNPE FTSLEAYEAH SDYLKMLDLT REMIQHAATA AYGEPVIWRH GEDGRPERVD
ISGQWPVKTV HQVVSEGAGE EVTPETPVEN LRRICDRLDI AHRPDWDAGQ VVLELYEHLG
EDRTTFPTFY TDFPTSTSPL TRAHRTRPGV AERWDLVAWG VELGTAYTEL TDPVEQRARL
TAQSVLAAGG DPEAMELDED FLQALEYAMP PTGGLGVGVD RVVMLITGQS IRESLAFPLA
KPQGDS
//
