ID D3F8H3_CONWI Unreviewed; 1118 AA.
AC D3F8H3;
DT 23-MAR-2010, integrated into UniProtKB/TrEMBL.
DT 23-MAR-2010, sequence version 1.
DT 27-MAR-2024, entry version 85.
DE RecName: Full=Lysine--tRNA ligase {ECO:0000256|HAMAP-Rule:MF_00252};
DE EC=6.1.1.6 {ECO:0000256|HAMAP-Rule:MF_00252};
DE AltName: Full=Lysyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_00252};
DE Short=LysRS {ECO:0000256|HAMAP-Rule:MF_00252};
GN Name=lysS {ECO:0000256|HAMAP-Rule:MF_00252};
GN OrderedLocusNames=Cwoe_2515 {ECO:0000313|EMBL:ADB50937.1};
OS Conexibacter woesei (strain DSM 14684 / CIP 108061 / JCM 11494 / NBRC
OS 100937 / ID131577).
OC Bacteria; Actinomycetota; Thermoleophilia; Solirubrobacterales;
OC Conexibacteraceae; Conexibacter.
OX NCBI_TaxID=469383 {ECO:0000313|EMBL:ADB50937.1, ECO:0000313|Proteomes:UP000008229};
RN [1] {ECO:0000313|EMBL:ADB50937.1, ECO:0000313|Proteomes:UP000008229}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14684 / CIP 108061 / JCM 11494 / NBRC 100937 / ID131577
RC {ECO:0000313|Proteomes:UP000008229};
RX PubMed=21304704;
RA Pukall R., Lapidus A., Glavina Del Rio T., Copeland A., Tice H.,
RA Cheng J.-F., Lucas S., Chen F., Nolan M., Bruce D., Goodwin L., Pitluck S.,
RA Mavromatis K., Ivanova N., Ovchinnikova G., Pati A., Chen A.,
RA Palaniappan K., Land M., Hauser L., Chang Y.-J., Jeffries C.D., Chain P.,
RA Meincke L., Sims D., Brettin T., Detter J.C., Rohde M., Goeker M.,
RA Bristow J., Eisen J.A., Markowitz V., Kyrpides N.C., Klenk H.-P.,
RA Hugenholtz P.;
RT "Complete genome sequence of Conexibacter woesei type strain (ID131577).";
RL Stand. Genomic Sci. 2:212-219(2010).
RN [2] {ECO:0000313|Proteomes:UP000008229}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14684 / CIP 108061 / JCM 11494 / NBRC 100937 / ID131577
RC {ECO:0000313|Proteomes:UP000008229};
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 Mikhailova N., Chertkov O., 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., Pukall R., Steenblock K., Schneider S., Klenk H.-P., Eisen J.A.;
RT "The complete genome of Conexibacter woesei DSM 14684.";
RL Submitted (JAN-2010) 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. {ECO:0000256|ARBA:ARBA00024681}.
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 Evidence={ECO:0000256|ARBA:ARBA00000367};
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 Evidence={ECO:0000256|ARBA:ARBA00000204, ECO:0000256|HAMAP-
CC Rule:MF_00252};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00252};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_00252};
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00252}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004651};
CC Multi-pass membrane protein {ECO:0000256|ARBA:ARBA00004651}. Cytoplasm
CC {ECO:0000256|HAMAP-Rule:MF_00252}. Membrane
CC {ECO:0000256|ARBA:ARBA00004141}; Multi-pass membrane protein
CC {ECO:0000256|ARBA:ARBA00004141}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000256|HAMAP-Rule:MF_00252}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the class-II
CC aminoacyl-tRNA synthetase family. {ECO:0000256|ARBA:ARBA00009968}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the LPG synthetase
CC family. {ECO:0000256|ARBA:ARBA00005270}.
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DR EMBL; CP001854; ADB50937.1; -; Genomic_DNA.
DR AlphaFoldDB; D3F8H3; -.
DR STRING; 469383.Cwoe_2515; -.
DR KEGG; cwo:Cwoe_2515; -.
DR eggNOG; COG1190; Bacteria.
DR eggNOG; COG2898; Bacteria.
DR HOGENOM; CLU_009016_0_0_11; -.
DR OrthoDB; 9802326at2; -.
DR Proteomes; UP000008229; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
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:0003676; F:nucleic acid binding; IEA:InterPro.
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; cd00775; LysRS_core; 1.
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 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; 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 {ECO:0000256|HAMAP-Rule:MF_00252,
KW ECO:0000313|EMBL:ADB50937.1};
KW Antibiotic resistance {ECO:0000256|ARBA:ARBA00023251};
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00252};
KW Ligase {ECO:0000256|HAMAP-Rule:MF_00252, ECO:0000313|EMBL:ADB50937.1};
KW Lipid metabolism {ECO:0000256|ARBA:ARBA00023098};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00252};
KW Membrane {ECO:0000256|SAM:Phobius};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Protein biosynthesis {ECO:0000256|HAMAP-Rule:MF_00252};
KW Reference proteome {ECO:0000313|Proteomes:UP000008229};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692, ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989,
KW ECO:0000256|SAM:Phobius}.
FT TRANSMEM 597..617
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 624..641
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 678..698
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 738..759
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 200..510
FT /note="Aminoacyl-transfer RNA synthetases class-II family
FT profile"
FT /evidence="ECO:0000259|PROSITE:PS50862"
FT REGION 1..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 510..551
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 11..27
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 525..545
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 422
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 429
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 429
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
SQ SEQUENCE 1118 AA; 122342 MW; F2D3D4F3EAD8C1E1 CRC64;
MAGVSATDEA PEADAETRDR GADFQEAERT RRLAKLDALR ERDVEPYPVR FDRDATAAEL
HDSFAELAPG TETGETVKVA GRVTALRRHG GLDFADLLDE TGTIQLLAER DELGEQALED
FAALDLGDWV GAEGTVVASK SGELTVRLAR FALLSKALRP LPDLRHGLTD PEARYRRRYV
DLVVNPRARA VFAARSVAIS AVRRVLTERG FREVETPVLL GQAGGAAAKP FLTHHNALDI
EMSLRIALEL PLKRLLVGGM DRVFEIGRVF RNEGLDTRHN PEFTLLEAYQ AFGDYSDMME
LTETLVSEAA LAANGTTVVR VGEREIDLRP PFRRARMTDL IKEHGGVEMH PSMPVEEARA
IADRFGVVWM DVWGSGKILA EVCDELCESK LIEPTFVMDH PREISPLARA HRDDPTLTER
FELVVAGREL ANAYSELNDP VDQAARFAYE AQQQAGGDEE AEPVDDDYVQ ALEYGLPPTG
GLGIGIDRLI MLITGVESIR DVILFPTLRP QEGGGQRAPT TATPPAALAA PPLPPAPPPA
DGEALAAPPP ESLRRPRALK PLAWLTAIVG VLSLLPSLPI ADWSFGFGEA LERPGRAATF
VISVVLGIAL IVVARQVARG KRRAWWIAMG LFGAATVVHV LKGPDPLAAL ANLAMLIAFV
WNRDAFRAKG DPGSLVDALA FIPIYVGVVL VFGVLSLMTQ ANNVTPELGT GGVLKTIGSG
LVGADGEYEY RRQLFGDFFA DALLALGIFG LAYLLYLLFR PLVQRTPPSD EWRAHAREIV
RRWGGDTLAY FALRKDKSYF FSTDGQSLIA YAYVRGYAMV AADPVGPPQD RARVLDEFLA
HCRGQGWGVA FLAVREADAP LYRERGMHAI YLGDEAILRC DTFTLKGKEM KAVREAVNRV
GREHSFELLR ESEATLELVA QLNAISAEWR RGSDERGFTM ELGEDVEGTD PDFVIALARD
AAGEPAGFLR FVPAYGEDLG YSLDLMRRKP DSLNGLTEFL IANAALELGA EGVRRLSLNF
AAWGRLLDTA EDAGLLGRFE RSVARGLNPY FQIQSLRDFN AKFGPQWLPR SIVIDDLGEL
PKVALLYASV EGFLDLPLIG RLFVPPVRRA VAEGSDAR
//
