ID A0A1H3RMM2_9PSEU Unreviewed; 1099 AA.
AC A0A1H3RMM2;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 27-MAR-2024, entry version 26.
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 ORFNames=SAMN05216215_105616 {ECO:0000313|EMBL:SDZ26926.1};
OS Saccharopolyspora shandongensis.
OC Bacteria; Actinomycetota; Actinomycetes; Pseudonocardiales;
OC Pseudonocardiaceae; Saccharopolyspora.
OX NCBI_TaxID=418495 {ECO:0000313|EMBL:SDZ26926.1, ECO:0000313|Proteomes:UP000199529};
RN [1] {ECO:0000313|EMBL:SDZ26926.1, ECO:0000313|Proteomes:UP000199529}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CGMCC 4.3530 {ECO:0000313|EMBL:SDZ26926.1,
RC ECO:0000313|Proteomes:UP000199529};
RA de Groot N.N.;
RL Submitted (OCT-2016) 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; FNOK01000056; SDZ26926.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1H3RMM2; -.
DR STRING; 418495.SAMN05216215_105616; -.
DR Proteomes; UP000199529; Unassembled WGS sequence.
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; 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 {ECO:0000256|HAMAP-Rule:MF_00252,
KW ECO:0000313|EMBL:SDZ26926.1};
KW Antibiotic resistance {ECO:0000256|ARBA:ARBA00023251};
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00252};
KW Cell membrane {ECO:0000256|ARBA:ARBA00022475};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00252};
KW Ligase {ECO:0000256|HAMAP-Rule:MF_00252};
KW Lipid metabolism {ECO:0000256|ARBA:ARBA00023098};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00252};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, 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 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 21..42
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 54..74
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 81..104
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 127..146
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 158..182
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 221..242
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 785..1089
FT /note="Aminoacyl-transfer RNA synthetases class-II family
FT profile"
FT /evidence="ECO:0000259|PROSITE:PS50862"
FT BINDING 1006
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 1013
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
FT BINDING 1013
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00252"
SQ SEQUENCE 1099 AA; 121315 MW; D5E4CCEFA2E4F41C CRC64;
MVQQEETAQR RWRSRMPSIT AGAVLVVAVL CVSSAVGLAL FGNVQPVRRF VDNVLFPAPP
NIAYGAFLAV LAAALKRRKR LALWILIGIL ALQVIGDIVV LVVLGDHIEA LWMDELGARY
HVPVDHVWFF STNIVVSALA FVPLWLSRGE FYGRAKRGSG YQAAVVFVLL IAVFVGLGYV
LVSLFPGSLR GAQARLTWTV ERVLGGAIDF NVTGFGHAPG WVNFVLGLFG TAALFTALFL
LLRAQRLAAA LRPEEERQVR RLIAEHGERD SLGYFATRRD KAVLFSDSGK AAVTYRVVAG
VCLASGDPLG DAEAWRPAIE KWLAMCREYT WTPAVMGVSE PGATAYARAG MKVLQLGDEA
VVYVAEFGLD GRDMRPVRQA VSRVERAGHT ARVRRHREVP AAEMAEIARL AEAWRDTESE
RGFSMALGRL GDPQDGDCVL VEAVSDRGEP VALLSLVPWG RNGLSLDLMR RDRDADNGVV
EFMVSSLVQA APRLGVERIS LNFAMFRAAF EEGARIGAGP VLRAWRGLLL FFSRWWQLES
LYRSNVKYRP HWFPRYVAFA ERRDLARVGI ASAIAEGFLP APRRESTSDE LVEVPALEAE
SEEAQRIGSQ QQQVRRDKLD ALRAAGVEPY PVAVPRTERC RAVTARHQDL LPDARTGEQV
SVAGRVVLLR DHGGVCFATL RDFSGDLQIM LTTKESGAEL QQAWRQQVDI GDQVSVTGEV
VASRRGELSV LAADWRLAAK CLHPLPDKHR GLVDPEARVR QRHVDLIMRP GARDALRSRG
AAVHALRETL VRSDFLEVET PMLQPVHGGA NARPFTTHSN AYDMRLYLRI APELYLKRLC
VGGVERLFEI GRNFRNEGVS HKHNPEFTML EAYQAFGDYT TMRELCRNLV LAAATAARGA
PTAIGPDGEF GLDGDWPVVP VNDAVSAALG EEITADTGLP RLQELCDAAS VPYEEHWERG
AVLLEMYERL VESRTAEPTF YTDFPADVSP LTRPHRDDPR LAERWDLVAF GTELGTGYSE
LVDPIEQRRR LTEQSLHAAG GDPEAMELDE DFLAALEYAM PPTGGLGLGV DRLIMLLTGG
SIRETLAFPL VRTDFAGRR
//
