ID LYSX_MYCTU Reviewed; 1172 AA.
AC P9WFU7; L0T8V2; P94974;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 27-MAR-2024, entry version 53.
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=Rv1640c;
GN ORFNames=MTCY06H11.04c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP FUNCTION IN THE PRODUCTION OF LYSINYLATED PHOSPHATIDYLGLYCEROL, AND ROLE IN
RP VIRULENCE.
RX PubMed=19649276; DOI=10.1371/journal.ppat.1000534;
RA Maloney E., Stankowska D., Zhang J., Fol M., Cheng Q.J., Lun S.,
RA Bishai W.R., Rajagopalan M., Chatterjee D., Madiraju M.V.;
RT "The two-domain LysX protein of Mycobacterium tuberculosis is required for
RT production of lysinylated phosphatidylglycerol and resistance to cationic
RT antimicrobial peptides.";
RL PLoS Pathog. 5:E1000534-E1000534(2009).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011445;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
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. {ECO:0000269|PubMed:19649276}.
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}.
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DR EMBL; AL123456; CCP44405.1; -; Genomic_DNA.
DR PIR; C70619; C70619.
DR RefSeq; NP_216156.1; NC_000962.3.
DR RefSeq; WP_003408102.1; NC_000962.3.
DR AlphaFoldDB; P9WFU7; -.
DR SMR; P9WFU7; -.
DR STRING; 83332.Rv1640c; -.
DR PaxDb; 83332-Rv1640c; -.
DR DNASU; 885428; -.
DR GeneID; 885428; -.
DR KEGG; mtu:Rv1640c; -.
DR PATRIC; fig|83332.111.peg.1825; -.
DR TubercuList; Rv1640c; -.
DR eggNOG; COG1190; Bacteria.
DR eggNOG; COG2898; Bacteria.
DR InParanoid; P9WFU7; -.
DR OrthoDB; 9801152at2; -.
DR BRENDA; 2.3.2.3; 3445.
DR BRENDA; 6.3.2.43; 3445.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; HDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
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; IBA:GO_Central.
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:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IDA:MTBBASE.
DR GO; GO:0046471; P:phosphatidylglycerol metabolic process; IDA:MTBBASE.
DR GO; GO:0008654; P:phospholipid biosynthetic process; IDA:MTBBASE.
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 1: Evidence at protein level;
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;
KW Virulence.
FT CHAIN 1..1172
FT /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT protein LysX"
FT /id="PRO_0000152657"
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
//
