ID A0A1C5K0E5_9ACTN Unreviewed; 1104 AA.
AC A0A1C5K0E5;
DT 02-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2016, sequence version 1.
DT 27-MAR-2024, entry version 34.
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=GA0074704_5299 {ECO:0000313|EMBL:SCG76290.1};
OS Micromonospora siamensis.
OC Bacteria; Actinomycetota; Actinomycetes; Micromonosporales;
OC Micromonosporaceae; Micromonospora.
OX NCBI_TaxID=299152 {ECO:0000313|EMBL:SCG76290.1, ECO:0000313|Proteomes:UP000198210};
RN [1] {ECO:0000313|EMBL:SCG76290.1, ECO:0000313|Proteomes:UP000198210}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 45097 {ECO:0000313|EMBL:SCG76290.1,
RC ECO:0000313|Proteomes:UP000198210};
RA Kjaerup R.B., Dalgaard T.S., Juul-Madsen H.R.;
RL Submitted (JUN-2016) 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}.
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DR EMBL; LT607751; SCG76290.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1C5K0E5; -.
DR Proteomes; UP000198210; Chromosome i.
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 ECO:0000313|EMBL:SCG76290.1};
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};
KW Lipid metabolism {ECO:0000256|ARBA:ARBA00023098};
KW Magnesium {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:UP000198210};
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 21..42
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 62..78
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 90..109
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 129..148
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 160..183
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 221..243
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 794..1096
FT /note="Aminoacyl-transfer RNA synthetases class-II family
FT profile"
FT /evidence="ECO:0000259|PROSITE:PS50862"
FT BINDING 1015
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 1022
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 1022
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
SQ SEQUENCE 1104 AA; 120394 MW; 6B35B33894E2E0C3 CRC64;
MTANDPHPGP GRDWLRQVPR AFATLLWVIA TVCALAALSS AVRSDIQPVR TFIDTLLLPA
PANLAYAVFL GTLASAVLRR KRLAYRVQVV YFSLSLLVGL VAGGLLLFVG AERLTDDAGQ
RIFNLIETVG VWVGVGFAAV ALTMLLAARR EFYARVRPGS TWRALAVFLG LAAAAVGLGY
LLLLVEPGSL VTWSDRLGYA AEKVFGGAVT LDLTRRGQAP AWVNLLLGAF GAAALVVGLF
TLLRSQRAAA VLHAGEEERI RALLARHGGR DSLGYFATRR DKAAIFSPSG KAAVTYRVVN
GVSLASGDPV GDPEAWGPAI RAWLAQAREY AWTPAVMGAS EAAARAYHRH GLKVLHLGDE
AILSTREFDL TGRDMRPVRQ AVHRVERAGY TSRVRRHADI PADELAEAAR LATRWRDTEH
ERGFSMALGR LGDPADGECV LVEAVDADGH VRAMLSLSPW GTDGVSLDLM RRDRTAENGV
MEFMVAALLG AGHRLGVERV SLNFAAFRSV FEQGARIGAG PVIRLWRGLL LFFSRWWQLE
SLYLSNAKYQ PHWTPRYLCF AERRELARVG LAAAVAEGFL ALPGGRPAPL QGVPPAGGGV
GFVPPADAAV HAVPPEPAEE RAPEQVLVRR AKLERLRADG VDPYPVGYPR TTSCADVRQR
HAGLAPDTGT GETVGVAGRV LLVRDHGRLC FVTIRDGSGD LQLLLEHDLD RWRSTVDVGD
HVGATGEVYA TRRGEVSVRV ADWRLTAKCL RPLPDKHHGL ADPEARVRQR YLDLAIDPGS
RELLRARGAA LHSLRGTLVG QGFLEVETPI LQRVHGGANA RPFVTHSNAY DLRLSLRIAP
ELYLKRLAVG GVERVYELGR AFRNEGVDHS HNPEFTVLEA YQAYADYHTM RELARELIVA
AAVAVHGAPV VRRPDGELVD IGGQWPTRTV DEAVSAALGE EVTPDTEVGV LRKLCDAARV
PYDPRWGRGE VLLELYERLV EARTGAPTFY LDFPTEVSPL TRPHRTDPRL AERWDLVAYG
MELGTAYSEL IDPVEQRRRL TEQSLKAAGG DPEAMELDED FLTALEYAMP PTGGLGLGVD
RLVMLLTGRS IRETLPFPLV RESS
//
