ID LYSX_RHOOB Reviewed; 1114 AA.
AC C1B7Z5;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 1.
DT 27-MAR-2024, entry version 97.
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; OrderedLocusNames=ROP_35510;
OS Rhodococcus opacus (strain B4).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae;
OC Rhodococcus.
OX NCBI_TaxID=632772;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=B4;
RA Takarada H., Sekine M., Hosoyama A., Yamada R., Fujisawa T., Omata S.,
RA Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.;
RT "Comparison of the complete genome sequences of Rhodococcus erythropolis
RT PR4 and Rhodococcus opacus B4.";
RL Submitted (MAR-2009) 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 (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}.
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DR EMBL; AP011115; BAH51798.1; -; Genomic_DNA.
DR RefSeq; WP_012690737.1; NC_012522.1.
DR AlphaFoldDB; C1B7Z5; -.
DR SMR; C1B7Z5; -.
DR STRING; 632772.ROP_35510; -.
DR KEGG; rop:ROP_35510; -.
DR PATRIC; fig|632772.20.peg.3720; -.
DR HOGENOM; CLU_008255_2_0_11; -.
DR OrthoDB; 9801152at2; -.
DR Proteomes; UP000002212; 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:0003677; F:DNA binding; IEA:UniProtKB-KW.
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: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; DNA-binding; Ligase; Lipid metabolism; Magnesium; Membrane;
KW Metal-binding; Multifunctional enzyme; Nucleotide-binding; Transferase;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..1114
FT /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT protein LysX"
FT /id="PRO_0000394335"
FT TRANSMEM 38..58
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 77..97
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 101..121
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 126..146
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 164..184
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 219..239
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DNA_BIND 674..751
FT /note="OB"
FT REGION 1..618
FT /note="Phosphatidylglycerol lysyltransferase"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 619..1114
FT /note="Lysine--tRNA ligase"
FT BINDING 1025
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1032
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1032
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1114 AA; 122292 MW; BAE0618F5814EB62 CRC64;
MSASTETHHA SEAAVPTAPR PRPALGSKSG RLHQVPHIAG LILGVFSVLV FLWSISPVLR
YYVHVPREYI DTYYFDAPDT SLSWALVVAL LAAALASRKR IAWWLLTIYL VLILITNVIV
SITDRNVNAM VAAVVQVVLI GILVAARPEF YTRVRRGAGW KALGVLIVGL AIGTLVGWGL
VELFPGTLPQ GERFLWALNR VTALAAADNE QFSGRPHGFV NTLLGLFGAM ALLAAVITLF
RAQRSHNALT GNDESALRGL LLQYGADDSL GYFATRRDKA VVFAPSGKAA ITYRVELGVC
LASGDPIGDP EAWPHAIEAW QTLASQYGWA TAVMGASETG ATAYNKAGLT VLQLGDEAIL
RTREFNLSGR DMRQVRQAVT RVRRQGVTVR IRRHRDVPPE EMAEAIRLAD AWRDTETERG
FSMALGRLGD RLDGDCLLVE AIAEDGEIDG ILSLVPWGPT GVSLDLMRRK PTSPNGVVEL
MVSELATTSD QFGITKVSLN FAVFRSVFEE GSRIGAGPIL RIWRSILVFF SRWWQLEALY
RSNVKYQPEW VPRFLCFDDN RELLRVGFAS AVAEGFVTLP RFGRSGTHDA IEHTGHHAAV
PAALVAAEGL HSDGSAPGEG LAPTATGPKR PEQVRVRLDK LTGLAEQGID PYPVAYPPSH
TVTEAVESPE GTTVRIAGRL LRIRDYGGVV FAVVRDWSGD IQVLVDEARV GTDRIRAFAA
EFDLGDLVEV AGVIGYSRRG ALSLLANEWR MTGKCLHPLP DKWKGLSDPE TRVRQRYVDL
AINTDARRLL EARSAVVKSL RDSLGGRGFL EVETPILQQV HGGANAAPFL THINAYNLDL
YLRIAPELYL KRLCVAGMEK VFEIGRVFRN EGVDFKHNPE FTILEAYEAH SDYEKMMVLC
RELIQTAAVA AYGREIIMRP GPDGTLVEVD ISGEWPVKTM HQAVAEKLGV DVSPETPLAE
LQRLCDEHEI PYQSTWDAGA VAQEMYEHLV EDYTEFPTFY TNFPTSMSPL TRPHPTIPGV
AAKWDLVAWG VELGTAYSEL TDPVDQRNRL TEQSMLAAGG DEEAMELDED FLQALEHAMP
PTGGLGMGVD RVVMLITGGS IRETLAFPLA KPRQ
//
