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LYSX_RHOOB
ID   LYSX_RHOOB              Reviewed;        1114 AA.
AC   C1B7Z5;
DT   18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT   26-MAY-2009, sequence version 1.
DT   03-AUG-2022, entry version 89.
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=ROP_35510;
OS   Rhodococcus opacus (strain B4).
OC   Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Rhodococcus.
OX   NCBI_TaxID=632772;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=B4;
RA   Takarada H., Sekine M., Hosoyama A., Yamada R., Fujisawa T., Omata S.,
RA   Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.;
RT   "Comparison of the complete genome sequences of Rhodococcus erythropolis
RT   PR4 and Rhodococcus opacus B4.";
RL   Submitted (MAR-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; AP011115; BAH51798.1; -; Genomic_DNA.
DR   RefSeq; WP_012690737.1; NC_012522.1.
DR   AlphaFoldDB; C1B7Z5; -.
DR   SMR; C1B7Z5; -.
DR   STRING; 632772.ROP_35510; -.
DR   EnsemblBacteria; BAH51798; BAH51798; ROP_35510.
DR   KEGG; rop:ROP_35510; -.
DR   PATRIC; fig|632772.20.peg.3720; -.
DR   HOGENOM; CLU_008255_2_0_11; -.
DR   OMA; DISGEWP; -.
DR   OrthoDB; 63621at2; -.
DR   Proteomes; UP000002212; 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; Transferase;
KW   Transmembrane; Transmembrane helix.
FT   CHAIN           1..1114
FT                   /note="Lysylphosphatidylglycerol biosynthesis bifunctional
FT                   protein LysX"
FT                   /id="PRO_0000394335"
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..28
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;  122292 MW;  BAE0618F5814EB62 CRC64;
     MSASTETHHA SEAAVPTAPR PRPALGSKSG RLHQVPHIAG LILGVFSVLV FLWSISPVLR
     YYVHVPREYI DTYYFDAPDT SLSWALVVAL LAAALASRKR IAWWLLTIYL VLILITNVIV
     SITDRNVNAM VAAVVQVVLI GILVAARPEF YTRVRRGAGW KALGVLIVGL AIGTLVGWGL
     VELFPGTLPQ GERFLWALNR VTALAAADNE QFSGRPHGFV NTLLGLFGAM ALLAAVITLF
     RAQRSHNALT GNDESALRGL LLQYGADDSL GYFATRRDKA VVFAPSGKAA ITYRVELGVC
     LASGDPIGDP EAWPHAIEAW QTLASQYGWA TAVMGASETG ATAYNKAGLT VLQLGDEAIL
     RTREFNLSGR DMRQVRQAVT RVRRQGVTVR IRRHRDVPPE EMAEAIRLAD AWRDTETERG
     FSMALGRLGD RLDGDCLLVE AIAEDGEIDG ILSLVPWGPT GVSLDLMRRK PTSPNGVVEL
     MVSELATTSD QFGITKVSLN FAVFRSVFEE GSRIGAGPIL RIWRSILVFF SRWWQLEALY
     RSNVKYQPEW VPRFLCFDDN RELLRVGFAS AVAEGFVTLP RFGRSGTHDA IEHTGHHAAV
     PAALVAAEGL HSDGSAPGEG LAPTATGPKR PEQVRVRLDK LTGLAEQGID PYPVAYPPSH
     TVTEAVESPE GTTVRIAGRL LRIRDYGGVV FAVVRDWSGD IQVLVDEARV GTDRIRAFAA
     EFDLGDLVEV AGVIGYSRRG ALSLLANEWR MTGKCLHPLP DKWKGLSDPE TRVRQRYVDL
     AINTDARRLL EARSAVVKSL RDSLGGRGFL EVETPILQQV HGGANAAPFL THINAYNLDL
     YLRIAPELYL KRLCVAGMEK VFEIGRVFRN EGVDFKHNPE FTILEAYEAH SDYEKMMVLC
     RELIQTAAVA AYGREIIMRP GPDGTLVEVD ISGEWPVKTM HQAVAEKLGV DVSPETPLAE
     LQRLCDEHEI PYQSTWDAGA VAQEMYEHLV EDYTEFPTFY TNFPTSMSPL TRPHPTIPGV
     AAKWDLVAWG VELGTAYSEL TDPVDQRNRL TEQSMLAAGG DEEAMELDED FLQALEHAMP
     PTGGLGMGVD RVVMLITGGS IRETLAFPLA KPRQ
 
 
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