ID LYSX_RHOE4 Reviewed; 1104 AA.
AC C0ZL89;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 1.
DT 27-MAR-2024, entry version 83.
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=RER_00710;
OS Rhodococcus erythropolis (strain PR4 / NBRC 100887).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae;
OC Rhodococcus; Rhodococcus erythropolis group.
OX NCBI_TaxID=234621;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PR4 / NBRC 100887;
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-2005) 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; AP008957; BAH30779.1; -; Genomic_DNA.
DR AlphaFoldDB; C0ZL89; -.
DR SMR; C0ZL89; -.
DR KEGG; rer:RER_00710; -.
DR eggNOG; COG1190; Bacteria.
DR eggNOG; COG2898; Bacteria.
DR HOGENOM; CLU_008255_2_0_11; -.
DR Proteomes; UP000002204; 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..1104
FT /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT protein LysX"
FT /id="PRO_0000394334"
FT TRANSMEM 25..45
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 64..84
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 90..110
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 117..137
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 151..171
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 205..225
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DNA_BIND 664..739
FT /note="OB"
FT REGION 1..608
FT /note="Phosphatidylglycerol lysyltransferase"
FT REGION 600..621
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 609..1104
FT /note="Lysine--tRNA ligase"
FT BINDING 1015
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1022
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1022
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1104 AA; 121729 MW; F4F70834C7EC08A6 CRC64;
MESPPENPRQ ARRFRKGRFS QVPHISGLIL GVFSVLVFLW SISPVLRHIL RVPREYIDSY
YFDAPDTSLS WALVVALLAA ALASRKRIAW WLLTIYLALI TLTNIASTIV DKNPNNAVAA
VVLLVVIGIL IAARPEFYTR VRRGAGWKAL GVLIGGMAVA TVIGWGLVEL FPGDLPQNQR
FLWALNRVTA AASVDNEVFD GHPRVFVNTV LGLLGAIALL AAVMTLFRAQ RSNNALTGND
ESAIRGLIQN FGADDSLAYF ATRRDKAVIF APSGKAAITY RVEIGVCLAS GDPIGDPEAW
PHAIEAWQDL ASQYGWATAV MGASETGATA YKKAGLSVLQ LGDEAILRTR EFNLNGRDMR
PVRQAVTRVR RHGVTVRMRR HRDIPPEDMA AVIIRADDWR DTDTERGFSM ALGRLGDHLD
GDCLLVEAVM GEGTEDESVV GMLSLVPWGP NGVSLDLMRR KPTAPNGVVE LMVSELATRS
DEIGVVRVSL NFAVFRSVFE EGSRIGAGPI LRIWRSVLVF FSRWWQLEAL YRSNVKYQPD
WEPRFLCFED NRELPRVGFA SAIAEGFVVL PSFGRKSSQV VKHTGTHAAV PAALVTSEGL
HADGSPPDSA PSFTTNGPRR PEQVRVRMNK LAQLADEGIA AYPVAYPPTH TIAAAAKSPE
GTRVRIAGRL LRVRDYGGVV FTDVRDWSGD IQVLVDQDNV GREKLAEFAA EFDLGDLIEV
SGTIGRSRKG ELSLIAVEWR MNGKCLHPLP DKWKGLSDPE TRVRQRYLDI ALNPKARELL
EARSAVVKSL RDSLGGRGYL EVETPILQQV HGGANAAPFL THINAYNLDL YLRIAPELYL
KRLCVAGMEK VFEIGRVFRN EGVDFKHNPE FTILEAYEAH SDYEGMMRMC RELIQAAAVA
AFGREIIMRP GPDGELVEVD ISGEWPVKTM HGAVAEKLGV DVSPETSLED LQKLCDANEI
PYQSSWDTGA IAQEMYEHLV EDYTEFPTFY TNFPTSMSPL TRPHRSIPGV AEKWDLVAWG
VELGTAYSEL TDPVDQRNRL TEQSMLAAGG DPEAMELDED FLQALEHAMP PTGGLGMGVD
RIVMLITGGS IRETLAFPLA KPRQ
//
