ID A0A6N7CWG9_9NOCA Unreviewed; 1113 AA. AC A0A6N7CWG9; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 27-NOV-2024, entry version 21. 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=lysX {ECO:0000313|EMBL:KAF0966059.1}; GN Synonyms=lysS {ECO:0000256|HAMAP-Rule:MF_00252}; GN ORFNames=MLGJGCBP_00786 {ECO:0000313|EMBL:KAF0966059.1}; OS Rhodococcus sp. T7. OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae; OC Rhodococcus. OX NCBI_TaxID=627444 {ECO:0000313|EMBL:KAF0966059.1, ECO:0000313|Proteomes:UP000471148}; RN [1] {ECO:0000313|EMBL:KAF0966059.1, ECO:0000313|Proteomes:UP000471148} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=T7 {ECO:0000313|EMBL:KAF0966059.1, RC ECO:0000313|Proteomes:UP000471148}; RA Ronen Z.; RT "Draft Genome Sequence of Rhodococcus sp. Strain YH1 and Rhodococcus sp. RT Strain T7 isolated from explosive contaminated environments."; RL Submitted (JAN-2020) 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:ARBA00000367}; 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: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}. 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:KAF0966059.1}. 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; WXYH01000024; KAF0966059.1; -; Genomic_DNA. DR AlphaFoldDB; A0A6N7CWG9; -. DR OrthoDB; 9801152at2; -. DR Proteomes; UP000471148; Unassembled WGS sequence. 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:0050071; F:phosphatidylglycerol lysyltransferase activity; IEA:UniProtKB-EC. 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; 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|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|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|ARBA:ARBA00022741, ECO:0000256|HAMAP- KW Rule:MF_00252}; Protein biosynthesis {ECO:0000256|HAMAP-Rule:MF_00252}; KW Reference proteome {ECO:0000313|Proteomes:UP000471148}; 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 37..60 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" FT TRANSMEM 80..95 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" FT TRANSMEM 102..122 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" FT TRANSMEM 128..145 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" FT TRANSMEM 157..180 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" FT TRANSMEM 218..239 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" FT DOMAIN 792..1111 FT /note="Aminoacyl-transfer RNA synthetases class-II family FT profile" FT /evidence="ECO:0000259|PROSITE:PS50862" FT REGION 1..21 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 1024 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252" FT BINDING 1031 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252" FT BINDING 1031 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252" SQ SEQUENCE 1113 AA; 122294 MW; F58C83C0F077E6E0 CRC64; MSASTETHHA SEADLTAPRP RPALGSKNGR LHQVPHIAGL ILGVFSVLVF LWSISPVLRY YVHVPREYID TYYFDAPDTS LSWALVVALL AAALASRKRI AWWLLTIYLT LILITNVIVS ITDRNVNAMV AAVVQVVLIG ILIAARPEFY TRVRRGAGWK ALGVLIVGLA IGTLVGWGLV ELFPGTLPQG ERFLWALNRV TALAAADNEQ FSGRPHGFVN TLLGLFGALA LLAAVITLFR AQRSHNALTG NDESALRGLL LQYGADDSLG YFATRRDKAV VFAPSGKAAI TYRVELGVCL ASGDPIGDPE AWPHAIEAWQ ALASQYGWAT AVMGASETGA TAYNKAGLTV LQLGDEAILR TREFNLSGRD MRQVRQAVTR VRRQGITVRI RRHRDVPPDE MAEAIRLADS WRDTETERGF SMALGRLGDR LDGDCLLVEA VAEDGEIDGI LSLVPWGPTG VSLDLMRRRP TSPNGVVELM VSELATNSDQ FGITKVSLNF AVFRSVFEEG SRIGAGPILR IWRSILVFFS RWWQLEALYR SNVKYQPEWV PRFLCFEDNR ELLRVGFASA VAEGFVTLPR FGRSGTHDAI EHTGHHAAVP AALVAAEGLH SDGSAPGEGL APTTTGPKRP EQVRVRLDKL AGLAEQGIDP YPVALPPSHT VTEAVESPEG TTVRIAGRLL RIRDYGGVVF AVVRDWSGDI QILVDEARVG TDRIRAFAAE FDLGDLVEVA GVIGYSRRGA LSLLANEWRM TGKCLHPLPD KWKGLSDPET RVRQRYVDLA INSDARRLLE ARSAVVKSLR DSLGGRGFLE VETPILQQVH GGANAAPFLT HINAYNLDLY LRIAPELYLK RLCVAGMEKV FEIGRVFRNE GVDFKHNPEF TILEAYEAHS DYEKMMVLCR ELIQTAAVAA YGREIIMRPG PDGRLVEVDI SGEWPVKTMH QAVAEKLGVD VSPETPLAEL QRLCDEHEIP YQSAWDAGAV AQEMYEHLVE DYTEFPTFYT NFPTSMSPLT RPHPTIPGVA AKWDLVAWGI ELGTAYSELT DPVDQRNRLT EQSMLAAGGD EEAMELDEDF LQALEHAMPP TGGLGMGVDR VVMLITGGSI RETLAFPLAK PRQ //