LYSX_RHOJR
ID LYSX_RHOJR Reviewed; 1114 AA.
AC Q0SAA3;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 03-AUG-2022, 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; OrderedLocusNames=RHA1_ro03733;
OS Rhodococcus jostii (strain RHA1).
OC Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Rhodococcus.
OX NCBI_TaxID=101510;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RHA1;
RX PubMed=17030794; DOI=10.1073/pnas.0607048103;
RA McLeod M.P., Warren R.L., Hsiao W.W.L., Araki N., Myhre M., Fernandes C.,
RA Miyazawa D., Wong W., Lillquist A.L., Wang D., Dosanjh M., Hara H.,
RA Petrescu A., Morin R.D., Yang G., Stott J.M., Schein J.E., Shin H.,
RA Smailus D., Siddiqui A.S., Marra M.A., Jones S.J.M., Holt R.,
RA Brinkman F.S.L., Miyauchi K., Fukuda M., Davies J.E., Mohn W.W.,
RA Eltis L.D.;
RT "The complete genome of Rhodococcus sp. RHA1 provides insights into a
RT catabolic powerhouse.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15582-15587(2006).
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; CP000431; ABG95533.1; -; Genomic_DNA.
DR RefSeq; WP_011596305.1; NC_008268.1.
DR AlphaFoldDB; Q0SAA3; -.
DR SMR; Q0SAA3; -.
DR STRING; 101510.RHA1_ro03733; -.
DR EnsemblBacteria; ABG95533; ABG95533; RHA1_ro03733.
DR KEGG; rha:RHA1_ro03733; -.
DR PATRIC; fig|101510.16.peg.3756; -.
DR eggNOG; COG1190; Bacteria.
DR eggNOG; COG2898; Bacteria.
DR HOGENOM; CLU_008255_2_0_11; -.
DR OMA; DISGEWP; -.
DR Proteomes; UP000008710; 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;
KW Reference proteome; Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..1114
FT /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT protein LysX"
FT /id="PRO_0000394336"
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..26
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; 122363 MW; 26A329864678E7FD CRC64;
MSASTETHHA SEAAVPTAPR PRPGLGTKNG RLHQVPHIAG LILGVFSVLV FLWSISPVLR
YYVHVPREYV DTYYFDAPDT SLSWALVVAL LAAALASRKR IAWWLLTIYL VLFLITNVIV
SITDKNVNAM AAAVVQVVLI GILIAARPEF YTRVRRGAGW KALGVLIVGL AIGTLLGWGL
VELFPGTLPQ NERFLWALNR VTALAAADNE QFTGRPHGFV NTLLGLFGAI ALLAAVITLF
RAQRSHNALT GNDESALRGL LLQYGADDSL GYFATRRDKA VVFAPSGKAA ITYRVELGVC
LASGDPIGDP EAWPHAIEEW QALASQYGWA TAVMGASETG ATAYNKAGLT VLQLGDEAIL
RTREFNLSGR DMRQVRQAVT RVRRQGVTVR IRRHRDVPAE EMAETIRLAD AWRDTETERG
FSMALGRLGD RLDGDCLLVE AVAEDGEIDG ILSLVPWGPT GVSLDLMRRK PTSPNGVVEL
MVSELATTSD QFGITKVSLN FAVFRSVFEE GSRIGAGPIL RIWRSILVFF SRWWQLEALY
RSNVKYQPEW VPRFLCFEDN RELLRVGFAS AVAEGFVTLP RFGRSGTRDA LEHTGTHAAV
PAALVAAEGL HSDGSAPGEG LAPTATGPKR PEQVRVRLDK LAGLAEQGID PYPVAYPPSH
TVTEAVESPE GTTVRIAGRL LRIRDYGGVV FAVVRDWSGD IQILVDEARV GTDRIRAFAA
EFDLGDLVEV AGVIGYSRRG ALSLLANEWR MTGKCLHPLP DKWKGLSDPE TRVRQRYVDL
AINSDARRLL EARSAVVKSL RDSLGGRGFL EVETPILQQV HGGANAAPFL THINAYNLDL
YLRIAPELYL KRLCVAGMEK VFEIGRVFRN EGVDFKHNPE FTILEAYEAH SDYEKMMVLC
RELIQTAAIA AYGREIIMRP GPDGALVEVD ISGEWPVKTM HQAVAEKLGV DVSPETPLTE
LQRLCDEHEI PYQSTWDAGA VAQEMYEHLV EDYTEFPTFY TNFPTSMSPL TRPHPTIPGV
AAKWDLVAWG VELGTAYSEL TDPVDQRNRL TEQSMLAAGG DEEAMELDED FLQALEHAMP
PTGGLGMGVD RVVMLITGGS IRETLAFPLA KPRQ
