ID   LYSX_MYCTO              Reviewed;        1172 AA.
AC   P9WFU6; L0T8V2; P94974;
DT   16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT   16-APR-2014, sequence version 1.
DT   03-AUG-2022, entry version 44.
DE   RecName: Full=Lysylphosphatidylglycerol biosynthesis bifunctional protein LysX;
DE   Includes:
DE     RecName: Full=Lysine--tRNA ligase;
DE              EC=6.1.1.6;
DE     AltName: Full=Lysyl-tRNA synthetase;
DE              Short=LysRS;
DE   Includes:
DE     RecName: Full=Phosphatidylglycerol lysyltransferase;
DE              EC=2.3.2.3;
DE     AltName: Full=Lysylphosphatidylglycerol synthetase;
DE              Short=LPG synthetase;
GN   Name=lysX; Synonyms=lysS2, lysU, mprF; OrderedLocusNames=MT1678;
OS   Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycobacterium; Mycobacterium tuberculosis complex.
OX   NCBI_TaxID=83331;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CDC 1551 / Oshkosh;
RX   PubMed=12218036; DOI=10.1128/jb.184.19.5479-5490.2002;
RA   Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O.,
RA   Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K.,
RA   Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L.,
RA   Delcher A., Utterback T.R., Weidman J.F., Khouri H.M., Gill J., Mikula A.,
RA   Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M.;
RT   "Whole-genome comparison of Mycobacterium tuberculosis clinical and
RT   laboratory strains.";
RL   J. Bacteriol. 184:5479-5490(2002).
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 (By similarity). {ECO:0000250}.
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   -!- 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   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000250};
CC   -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Multi-pass membrane
CC       protein {ECO:0000305}.
CC   -!- MISCELLANEOUS: There are two lysyl-tRNA ligases in M.tuberculosis.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the LPG synthetase
CC       family. {ECO:0000305}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the class-II
CC       aminoacyl-tRNA synthetase family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAK45947.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; AE000516; AAK45947.1; ALT_INIT; Genomic_DNA.
DR   PIR; C70619; C70619.
DR   RefSeq; WP_003408102.1; NZ_KK341227.1.
DR   AlphaFoldDB; P9WFU6; -.
DR   SMR; P9WFU6; -.
DR   EnsemblBacteria; AAK45947; AAK45947; MT1678.
DR   KEGG; mtc:MT1678; -.
DR   PATRIC; fig|83331.31.peg.1804; -.
DR   HOGENOM; CLU_008255_2_0_11; -.
DR   Proteomes; UP000001020; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-UniRule.
DR   GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR   GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0004824; F:lysine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0050071; F:lysyltransferase activity; IEA:UniProtKB-EC.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
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; -; 1.
DR   Gene3D; 3.30.930.10; -; 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   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; SSF50249; SSF50249; 1.
DR   SUPFAM; SSF55681; SSF55681; 1.
DR   TIGRFAMs; TIGR00499; lysS_bact; 1.
DR   PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE   3: Inferred from homology;
KW   Aminoacyl-tRNA synthetase; Antibiotic resistance; ATP-binding;
KW   Cell membrane; DNA-binding; Ligase; Lipid metabolism; Magnesium; Membrane;
KW   Metal-binding; Multifunctional enzyme; Nucleotide-binding; Transferase;
KW   Transmembrane; Transmembrane helix; Virulence.
FT   CHAIN           1..1172
FT                   /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT                   protein LysX"
FT                   /id="PRO_0000428475"
FT   TRANSMEM        80..100
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        122..142
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        146..166
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        177..197
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        214..234
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        272..292
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        497..517
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        612..632
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   DNA_BIND        726..804
FT                   /note="OB"
FT   REGION          1..663
FT                   /note="Phosphatidylglycerol lysyltransferase"
FT   REGION          1..34
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          664..1172
FT                   /note="Lysine--tRNA ligase"
FT   COMPBIAS        19..34
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         1084
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         1091
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         1091
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1172 AA;  128240 MW;  97E91546A1ACCAEB CRC64;
     MGLHLTVPGL RRDGRGVQSN SHDTSSKTTA DISRCPQHTD AGLQRAATPG ISRLLGISSR
     SVTLTKPRSA TRGNSRYHWV PAAAGWTVGV IATLSLLASV SPLIRWIIKV PREFINDYLF
     NFPDTNFAWS FVLALLAAAL TARKRIAWLV LLANMVLAAV VNAAEIAAGG NTAAESFGEN
     LGFAVHVVAI VVLVLGYREF WAKVRRGALF RAAAVWLAGA VVGIVASWGL VELFPGSLAP
     DERLGYAANR VVGFALADPD LFTGRPHVFL NAIFGLFGAF ALIGAAIVLF LSQRADNALT
     GEDESAIRGL LDLYGKDDSL GYFATRRDKS VVFASSGRAC ITYRVEVGVC LASGDPVGDH
     RAWPQAVDAW LRLCQTYGWA PGVMGASSQG AQTYREAGLT ALELGDEAIL RPADFKLSGP
     EMRGVRQAVT RARRAGLTVR IRRHRDIAED EMAQTITRAD SWRDTETERG FSMALGRLGD
     PADSDCLLVE AIDPHNQVLA MLSLVPWGTT GVSLDLMRRS PQSPNGTIEL MVSELALHAE
     SLGITRISLN FAVFRAAFEQ GAQLGAGPVA RLWRGLLVFF SRWWQLETLY RSNMKYQPEW
     VPRYACYEDA RVIPRVGVAS VIAEGFLVLP FSRRNRVHTG HHPAVPERLA ATGLLHHDGS
     APDVSGLRQV GLTNGDGVER RLPEQVRVRF DKLEKLRSSG IDAFPVGRPP SHTVAQALAA
     DHQASVSVSG RIMRIRNYGG VLFAQLRDWS GEMQVLLDNS RLDQGCAADF NAATDLGDLV
     EMTGHMGASK TGTPSLIVSG WRLIGKCLRP LPNKWKGLLD PEARVRTRYL DLAVNAESRA
     LITARSSVLR AVRETLFAKG FVEVETPILQ QLHGGATARP FVTHINTYSM DLFLRIAPEL
     YLKRLCVGGV ERVFELGRAF RNEGVDFSHN PEFTLLEAYQ AHADYLEWID GCRELIQNAA
     QAANGAPIAM RPRTDKGSDG TRHHLEPVDI SGIWPVRTVH DAISEALGER IDADTGLTTL
     RKLCDAAGVP YRTQWDAGAV VLELYEHLVE CRTEQPTFYI DFPTSVSPLT RPHRSKRGVA
     ERWDLVAWGI ELGTAYSELT DPVEQRRRLQ EQSLLAAGGD PEAMELDEDF LQAMEYAMPP
     TGGLGMGIDR VVMLITGRSI RETLPFPLAK PH