ID LYSX_NOCFA Reviewed; 1128 AA.
AC Q5Z3P6;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 18-MAY-2010, sequence version 2.
DT 27-MAR-2024, entry version 122.
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; OrderedLocusNames=NFA_1030;
OS Nocardia farcinica (strain IFM 10152).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae;
OC Nocardia.
OX NCBI_TaxID=247156;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IFM 10152;
RX PubMed=15466710; DOI=10.1073/pnas.0406410101;
RA Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K.,
RA Shiba T., Hattori M.;
RT "The complete genomic sequence of Nocardia farcinica IFM 10152.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004).
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 -!- 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=BAD54945.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP006618; BAD54945.1; ALT_INIT; Genomic_DNA.
DR AlphaFoldDB; Q5Z3P6; -.
DR SMR; Q5Z3P6; -.
DR STRING; 247156.NFA_1030; -.
DR KEGG; nfa:NFA_1030; -.
DR eggNOG; COG1190; Bacteria.
DR eggNOG; COG2898; Bacteria.
DR HOGENOM; CLU_008255_2_0_11; -.
DR Proteomes; UP000006820; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-UniRule.
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; Antibiotic resistance; ATP-binding;
KW Cell membrane; Ligase; Lipid metabolism; Magnesium; Membrane;
KW Metal-binding; Multifunctional enzyme; Nucleotide-binding;
KW Reference proteome; Transferase; Transmembrane; Transmembrane helix;
KW Virulence.
FT CHAIN 1..1128
FT /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT protein LysX"
FT /id="PRO_0000394333"
FT TRANSMEM 55..75
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 97..117
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 121..141
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 147..167
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 184..204
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 240..260
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REGION 1..632
FT /note="Phosphatidylglycerol lysyltransferase"
FT REGION 1..47
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 619..644
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 633..1128
FT /note="Lysine--tRNA ligase"
FT BINDING 1040
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1047
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1047
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1128 AA; 124152 MW; 08A3244F5F32D454 CRC64;
MDNPPPTGVA PRHLPPGSVH TGKVTASLSH RRPDSVQDAP PAPVPHRAHG RLREVPHIAG
LVLGVFAVAC LLWSLSPALR FLTGPPRRFV DDYYFDAPDT NVMWALIVGL LAGAIASRKR
IAWWLLVGYL TLFAVANGLR FAAEQNINAL VAMIVQVGVV GLLIAAWPEF YTRVRRGAGW
KALGVLVGGL AIGCLLGWGL VEVFPGSLPP GWQRPGWAVY RVTAAILVEN EHFGGHPRPF
VNVLLGLFGA IALLAAVLTL LRSQRAANAM TGLDESAIRG LLEHSDVEDS LGYFATRRDK
AVVFAPSGKA AVTYRVELGV CLASGDPVGV REAWPHAIDA WLRLADRFGW TPAVMGASEE
GATAYRRAGL SALRLGDEAV LDTRDFSLAG PELRQVRQAA NRLRKQGVRV RIRRHREIPS
AEFEQIMARA DAWRDTETER GFSMALGRLG DPLDADCLLV EAVAADDRVL GMLSLVPWGR
TGVSLELMRR DPQGPNGVME LMISQLALNS EQFGITRVSL NFAVFRSVFE EGGRIGAGPV
LRLWRGVLLF FSRWWQLEAL YRSNVKYQPD WVPRFFLFEE RRQLPRVAVA SALAEGFLPR
LGKDPDASAH TGAQSAVPDT LTGLHADGSP PDWPKPDLLD SGPRRPEQVR VRMAKLDRMT
AAGVDAYPVA YPPTHTVAAA RRSPRGTTVR VCGRLLRIRD YGGVVFALLR DWSDDIQLVI
DRERVGAARS AEFGEYFDLG DLIEVSGQIG RSRSGELSLL AADWRMLGKC LHPLPDKWKG
LADPEARVRQ RYVDMAINPE TRDVLAKRSA VVRSLRESLN SWGYLEVETP ILQQVHGGAN
ATPFTTHINA YDLDLYLRIA PELYLKRLCV GGMEKVFELG RTFRNEGVDF SHNPEFTILE
AYEAHSDYIR MMHTCRVLIQ NAALAANGSM VAMRPGADGA LEPVDISGDW PVKTVHGAVS
AAVGTEITPR TGVAELRELC DRVGVPYQHG WDEGQIVLEM YEHLVEARTE EPTFYVDFPT
SVSPLTRAHR STPGVTERWD LVAWGVELGT AYSELTDPVE QRRRLTEQSV LAANGDPEAM
ELDEDFLQAL EHAMPPTGGL GMGVDRIVML ITGRSIRETL PFPLVKPR
//
