LYSX_GORB4
ID LYSX_GORB4 Reviewed; 1138 AA.
AC D0LB45;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2009, sequence version 1.
DT 03-AUG-2022, entry version 74.
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=Gbro_0127;
OS Gordonia bronchialis (strain ATCC 25592 / DSM 43247 / BCRC 13721 / JCM 3198
OS / KCTC 3076 / NBRC 16047 / NCTC 10667) (Rhodococcus bronchialis).
OC Bacteria; Actinobacteria; Corynebacteriales; Gordoniaceae; Gordonia.
OX NCBI_TaxID=526226;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25592 / DSM 43247 / BCRC 13721 / JCM 3198 / KCTC 3076 / NBRC
RC 16047 / NCTC 10667;
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Kyrpides N., Mavromatis K., Ivanova N.,
RA Ovchinnikova G., Saunders E., Brettin T., Detter J.C., Han C., Larimer F.,
RA Land M., Hauser L., Markowitz V., Cheng J.-F., Hugenholtz P., Woyke T.,
RA Wu D., Jando M., Schneider S., Goeker M., Klenk H.-P., Eisen J.A.;
RT "The complete chromosome of Gordonia bronchialis DSM 43247.";
RL Submitted (OCT-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; CP001802; ACY19476.1; -; Genomic_DNA.
DR RefSeq; WP_012832068.1; NC_013441.1.
DR AlphaFoldDB; D0LB45; -.
DR SMR; D0LB45; -.
DR STRING; 526226.Gbro_0127; -.
DR PRIDE; D0LB45; -.
DR EnsemblBacteria; ACY19476; ACY19476; Gbro_0127.
DR KEGG; gbr:Gbro_0127; -.
DR eggNOG; COG1190; Bacteria.
DR eggNOG; COG2898; Bacteria.
DR HOGENOM; CLU_008255_2_1_11; -.
DR OMA; DISGEWP; -.
DR OrthoDB; 63621at2; -.
DR Proteomes; UP000001219; 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;
KW Virulence.
FT CHAIN 1..1138
FT /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT protein LysX"
FT /id="PRO_0000394314"
FT TRANSMEM 56..76
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 92..112
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 119..139
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 155..175
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 190..210
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 247..267
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DNA_BIND 698..772
FT /note="OB"
FT REGION 1..646
FT /note="Phosphatidylglycerol lysyltransferase"
FT REGION 1..34
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 647..1138
FT /note="Lysine--tRNA ligase"
FT COMPBIAS 1..19
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 1048
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1055
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 1055
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1138 AA; 125686 MW; 7D3EC6EE66800C13 CRC64;
MALDTPSSDL PVSTDDTAEH QPTPAHRPPS AADRRSVDLL EKIRRPRGFG AGAPKIAGTV
VGVLAGIALL SSIFPLFRRL IHYPRDFIDN YIVSLPNTSL AWAFVLALVA IALSSRKRIA
WWIATIYLVL FMVSNALLLV DPVATDFGVD TDERIQIWIG LGIDAAALIF LIVTYRQFYT
RVRRGALFRA LGVLIVGLTA ATLVGWGLVW AWPGSLERTE RLPYAFNRVV TFGSIDSRTF
DGHHTHIVID SALGLLGALA LIAAATVLFR SQRLESLMTS DDEKLIRALI TRFNDDDSLA
YFSTRRDKAV VFSPDGRAAI TYRVEIGVGL AGGDPIGDPE SWPDAIAEFL TLCDRYGWHP
AAMGSSARGA AAYDAAGFGS LSIGDEAILH TREYTISGPA MKAVRQAVTR TRRAGVTVRI
RRHGEVPDDE MPQVIARADA WRDTDEERGF AMALSRLGDR ADDDCLLVEA VEHAGTPEEK
VIGMLSFVPW GRRGVSLDVM RRDRGSVNGV VETMVTELCR NSEQFGITEI SLNFATFRAF
FEQGPQIGAG PIMRLGYSVL MFGSRFFQME SLYKSNAKYL PDWQPRFLCF EDNRILPRVG
LAAIVTEGFV QLPRFGRKQH YIAGQSSIPA GVDADALIAQ LESEEDRTAV EVHRPEQVRV
RVAKLDRLIE EGFDPYPPAD APTHTIAEAI AEPEGTQVTI AGRVTKMRDF GKVTFADVHD
WSGQIQMLVE ASRVIPGTPD FGSDVDLGDL VEARGVIGRS RSGELSVLID AWRFNGKCLR
PLPDKWSGLT DPEARVRQRY VDLAINPRSR ELLATRSVVV KALRDFLADR GFMEVETPIL
QQIHGGANAT PFQTHINAYN LDLYLRIAPE LYLKRLCVGG VEKVFEIGRN FRNEGVDFSH
NPEFTSLEAY AAHSDYLKML DLTREMIQHA ATAAHGEPVI IRVDDEGNEQ RVDISGDWPV
RTVHEVVSEG AGVEITSDTE VSELRGICDR LEIAYRPDWD AGQIVLELYE HLGEDRTTVP
TFYTDFPTST SPLTRAHRSK PGVAERWDLV AWGVELGTAY TELTDPVEQR KRLTAQSILA
ADGDPEAMEL DEDFLTALEY AMPPTGGLGV GVDRVVMLIT GQSIRESLAF PMVKPTDA
