ID   A0AAC9AN68_9ACTN        Unreviewed;      1081 AA.
AC   A0AAC9AN68;
DT   29-MAY-2024, integrated into UniProtKB/TrEMBL.
DT   29-MAY-2024, sequence version 1.
DT   05-FEB-2025, entry version 5.
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=AXH35_04755 {ECO:0000313|EMBL:AMS04886.1};
OS   Acidipropionibacterium acidipropionici.
OC   Bacteria; Bacillati; Actinomycetota; Actinomycetes; Propionibacteriales;
OC   Propionibacteriaceae; Acidipropionibacterium.
OX   NCBI_TaxID=1748 {ECO:0000313|EMBL:AMS04886.1, ECO:0000313|Proteomes:UP000075221};
RN   [1] {ECO:0000313|EMBL:AMS04886.1, ECO:0000313|Proteomes:UP000075221}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 55737 {ECO:0000313|EMBL:AMS04886.1,
RC   ECO:0000313|Proteomes:UP000075221};
RA   Luna Flores C.H., Nielsen L.K., Marcellin E.;
RT   "Complete Genome Sequence of Propionibacterium acidipropionici ATCC
RT   55737.";
RL   Submitted (FEB-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=L-lysyl-tRNA(Lys) + a 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-
CC         glycerol) = a 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:ARBA00047540};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=tRNA(Lys) + L-lysine + ATP = L-lysyl-tRNA(Lys) + AMP +
CC         diphosphate; 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:ARBA00048573, 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}.
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   ---------------------------------------------------------------------------
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; CP014352; AMS04886.1; -; Genomic_DNA.
DR   RefSeq; WP_062819224.1; NZ_CP031057.1.
DR   Proteomes; UP000075221; Chromosome.
DR   GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
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:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR   GO; GO:0000049; F:tRNA binding; IEA:TreeGrafter.
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; 3.30.930.10; Bira Bifunctional Protein, Domain 2; 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:SF15; LYSINE--TRNA LIGASE, CHLOROPLASTIC_MITOCHONDRIAL; 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|ARBA:ARBA00023146,
KW   ECO:0000256|HAMAP-Rule:MF_00252};
KW   Antibiotic resistance {ECO:0000256|ARBA:ARBA00023251};
KW   ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW   Rule:MF_00252}; Cell membrane {ECO:0000256|ARBA:ARBA00022475};
KW   Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00252};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, 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|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_00252}; Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW   Rule:MF_00252}; Protein biosynthesis {ECO:0000256|HAMAP-Rule:MF_00252};
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        25..48
FT                   /note="Helical"
FT                   /evidence="ECO:0000256|SAM:Phobius"
FT   TRANSMEM        60..82
FT                   /note="Helical"
FT                   /evidence="ECO:0000256|SAM:Phobius"
FT   TRANSMEM        102..123
FT                   /note="Helical"
FT                   /evidence="ECO:0000256|SAM:Phobius"
FT   TRANSMEM        135..156
FT                   /note="Helical"
FT                   /evidence="ECO:0000256|SAM:Phobius"
FT   DOMAIN          755..1077
FT                   /note="Aminoacyl-transfer RNA synthetases class-II family
FT                   profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50862"
FT   BINDING         990
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT   BINDING         997
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT   BINDING         997
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
SQ   SEQUENCE   1081 AA;  117795 MW;  41737D41C53FDE11 CRC64;
     MLVGAVLLIG RMLFQQTWWV SALATGFSIV VFPIDGGGWG LVVLLLILAA GLNRRKRLSW
     AVCLGLFGLM WVVSLLFFGV LIAEVAGGEP TRIHDDVEMA GYVFNTFSVG AILVALIVHH
     GRFGARTARA NVRPALATLV GGLAATVLIG WLLVWATGGQ GRPRNRLWRL ISELLRGNRS
     QVAPPSPIWV ENIVELLAAI TLATAFIMLL RSQRQVAVLG LGDELELRNL LDENPSDSLG
     YFALRRDKAV VFSPDRRAAV CYRAVAGVAL ASGDPVGPRA QWPAAIDAFL TVAHTYGWSP
     AVVGASEEGA TAWQGAGLRV TRIGDEAIIS PSTFDLQSRD LRGVRSVVNR LRRSGYTVRV
     RRHSDIEPDE LSRLIALADA WRADGEERGF SMALSRLGDP LDGDCVMVEA LYPAGDIRGD
     GSTAGLLSFV PWGGDGLSLD VMRHDPRADN GVTELMVAGL MATGRELGLH RVSLNFAVFR
     EVIEEGSRVG ARPLQRLAAR FVSGVSRWFQ IEQLYRSNVK YAPDWQARYL GYADAGELAQ
     VGLALGLAEG QIDLPRILRP APPPAQPIYS VAAHPEIAAV LERQRPDVEL PGRRVGEQMR
     HRQQTRERII AAGGEAYPPD IHPSGAPGDL ATAAEGGELS LVGRVAGVRD HGGVIFADLT
     DWSGTAQILL DASALGAPAM DRWRADISLG DHVLVGGRAG SSRNGTRSLL AGEFRLAAKA
     LHPLPDRRSG MSDPEEKVRR RYLDLIVNPA ARDELRARSQ AIRAVRETLL SHDFLEVETP
     ILQTIHGGAN ARPFRTHINA YDLDLYLRIA PELYLKRLMV GGAGRVFEIG RNFRNEGADA
     THNPEFTMLE AYQAYGDYVQ MRHLTREMIL AASRRATGGT VIHGRDADGV EHEMDLAEEW
     RVITVNEGIS AALGEEVTAD TPKETLVGYA EKLGIAVSPK WDRGDVVLEL HEHLSERTTV
     GPTFFCDFPA DVSPLTRQHR DDPRLAEKWD LIVLGDEVAT AYTELVDPVI QRERFTAQSL
     RAAGGDPEAM ELDEDFLEAL EYAMPPTGGM GMGLDRLVML LTGASIRQTI TFPLVRPRSS
     S
//