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Protein

Lysylphosphatidylglycerol biosynthesis bifunctional protein LysX

Gene

lysX

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the production of L-lysyl-tRNA(Lys)transfer and the transfer of a lysyl group from L-lysyl-tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG), one of the components of the bacterial membrane with a positive net charge. LPG synthesis contributes to the resistance to cationic antimicrobial peptides (CAMPs) and likely protects M.tuberculosis against the CAMPs produced by competiting microorganisms (bacteriocins). In fact, the modification of anionic phosphatidylglycerol with positively charged L-lysine results in repulsion of the peptides (By similarity).By similarity

Catalytic activityi

ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
L-lysyl-tRNA(Lys) + phosphatidylglycerol = tRNA(Lys) + 3-O-L-lysyl-1-O-phosphatidylglycerol.

Cofactori

Mg2+By similarityNote: Binds 3 Mg2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1018 – 10181Magnesium 1By similarity
Metal bindingi1025 – 10251Magnesium 1By similarity
Metal bindingi1025 – 10251Magnesium 2By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase, Transferase

Keywords - Biological processi

Antibiotic resistance, Lipid metabolism

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMSME246196:GJ4Y-3795-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysylphosphatidylglycerol biosynthesis bifunctional protein LysX
Including the following 2 domains:
Lysine--tRNA ligase (EC:6.1.1.6)
Alternative name(s):
Lysyl-tRNA synthetase
Short name:
LysRS
Phosphatidylglycerol lysyltransferase (EC:2.3.2.3)
Alternative name(s):
Lysylphosphatidylglycerol synthetase
Short name:
LPG synthetase
Gene namesi
Name:lysX
Synonyms:lysS2
Ordered Locus Names:MSMEG_3796, MSMEI_3707
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
Proteomesi
  • UP000006158 Componenti: Chromosome
  • UP000000757 Componenti: Chromosome

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei18 – 3821HelicalSequence analysisAdd
BLAST
Transmembranei59 – 7921HelicalSequence analysisAdd
BLAST
Transmembranei87 – 10721HelicalSequence analysisAdd
BLAST
Transmembranei117 – 13721HelicalSequence analysisAdd
BLAST
Transmembranei155 – 17521HelicalSequence analysisAdd
BLAST
Transmembranei210 – 23021HelicalSequence analysisAdd
BLAST
Transmembranei307 – 32721HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11061106Lysylphosphatidylglycerol biosynthesis bifunctional protein LysXPRO_0000394324Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi246196.MSMEG_3796.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 603603Phosphatidylglycerol lysyltransferaseAdd
BLAST
Regioni604 – 1106503Lysine--tRNA ligaseAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the LPG synthetase family.Curated
In the C-terminal section; belongs to the class-II aminoacyl-tRNA synthetase family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105CRK. Bacteria.
COG1190. LUCA.
COG2898. LUCA.
HOGENOMiHOG000046227.
KOiK04567.
OrthoDBiEOG69PQ2M.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_00252. Lys_tRNA_synth_class2.
InterProiIPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR024320. LPG_synthase_C.
IPR002313. Lys-tRNA-ligase_II.
IPR018149. Lys-tRNA-synth_II_C.
IPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
IPR031553. tRNA-synt_2_TM.
[Graphical view]
PANTHERiPTHR22594. PTHR22594. 1 hit.
PfamiPF09924. DUF2156. 1 hit.
PF00152. tRNA-synt_2. 1 hit.
PF16995. tRNA-synt_2_TM. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view]
PRINTSiPR00982. TRNASYNTHLYS.
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00499. lysS_bact. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A0QYV1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTVISRVEHL PARPASRVAW VPAAAGWTVG VIATLSLIAS VSPLVRSLIR
60 70 80 90 100
VPREFVNDFI FNFPDTSFAW AFVLALLAAA LAARKRIAWW VLVLYLVGAI
110 120 130 140 150
GWNVGDLAAG GDTVADDIGE LIGIAFHVAA IVFLVVARKE FWAKVRRGAL
160 170 180 190 200
LKSAAVLVAG NLIGIVVAWG LLQAFPGTLD PEWRLPYAVN RVSGFATVPT
210 220 230 240 250
EVFEGYSHTF LNAIFGLFGA LALMAAAIVL FQSQRASNAL TGEDESAIRG
260 270 280 290 300
LLELYGKNDS LGYFATRRDK SVVFAPNGRA AITYRVEVGV CLASGDPVGD
310 320 330 340 350
PKSWPQAIAA WLQLCQAYGW APGVMGASLA GAEAYRAAGL NALQLGDEAI
360 370 380 390 400
LHPDRFRLSG PDMRAVRQAV TRARRAGTSV RIRRHRELSP EEMAAVIRRA
410 420 430 440 450
DAWRDTETER GFSMALGRLG DPADDDCLLV EAVQGDEVVA MLSLVPWGSN
460 470 480 490 500
GVSLDVMRRS PRSPNGTIEL MVSELCMQAE DIGISRISLN FAMFRSAFEQ
510 520 530 540 550
GAQLGAGPVA RLWRALLVFF SKWWQLESLY RSNMKYQPEW VPRYACYEDA
560 570 580 590 600
RLVPRVGVAS VIAEGFLVLP FSRRNKQHTG EHIAAPDTLV QSGRLHRDGS
610 620 630 640 650
APDVTGLQGE LPDADDEPRL PEQVRVRMAK LKALQGNGVD AYPVGQPPSH
660 670 680 690 700
TVAQALGATD GETLSVAGRV MRIRDYGGVL FAQLRDWSGE VQLLLDNAAL
710 720 730 740 750
TEGETADFTA TIDLGDLVEV TGSMGFSRNG TRSLLVERWR LIGKCLRPLP
760 770 780 790 800
DKWKGLTDQE ARVRARYVDL AVNTEARDLI RARSGALHAI RETLYSKGFL
810 820 830 840 850
EVETPILQQI HGGANARPFL THINAYDLDL YLRIAPELYL KRLCVGGVER
860 870 880 890 900
VFELGRAFRN EGVDFSHNPE FTLLEAYQAH ADYNVWIDGC RELIQNAAQA
910 920 930 940 950
ANGAQVFLRP RPNDPAGTLE PVDISGQWAV KTVHDAVSEA IGEHITPETE
960 970 980 990 1000
LGELRRLCDS AGIPYLTHWD AGAVVLEMYE HLVEDRTTEP TFYKDFPTSV
1010 1020 1030 1040 1050
SPLTRPHRSI PGVAERWDLV AWGVELGTAY SELTDPVEQR RRLQEQSLLA
1060 1070 1080 1090 1100
AGGDPEAMEL DEDFLQAMEY AMPPTGGLGM GVDRVVMMIT GRSIRETLPF

PLAKPR
Length:1,106
Mass (Da):121,219
Last modified:May 18, 2010 - v2
Checksum:iF4D0E0822E5F2AF9
GO

Sequence cautioni

The sequence ABK71122.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK71122.1. Different initiation.
CP001663 Genomic DNA. Translation: AFP40166.1.
RefSeqiWP_014877820.1. NZ_CP009494.1.
YP_888089.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK71122; ABK71122; MSMEG_3796.
AFP40166; AFP40166; MSMEI_3707.
GeneIDi4537473.
KEGGimsb:LJ00_18855.
msg:MSMEI_3707.
msm:MSMEG_3796.
PATRICi18079983. VBIMycSme59918_3734.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK71122.1. Different initiation.
CP001663 Genomic DNA. Translation: AFP40166.1.
RefSeqiWP_014877820.1. NZ_CP009494.1.
YP_888089.1. NC_008596.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_3796.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK71122; ABK71122; MSMEG_3796.
AFP40166; AFP40166; MSMEI_3707.
GeneIDi4537473.
KEGGimsb:LJ00_18855.
msg:MSMEI_3707.
msm:MSMEG_3796.
PATRICi18079983. VBIMycSme59918_3734.

Phylogenomic databases

eggNOGiENOG4105CRK. Bacteria.
COG1190. LUCA.
COG2898. LUCA.
HOGENOMiHOG000046227.
KOiK04567.
OrthoDBiEOG69PQ2M.

Enzyme and pathway databases

BioCyciMSME246196:GJ4Y-3795-MONOMER.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_00252. Lys_tRNA_synth_class2.
InterProiIPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR024320. LPG_synthase_C.
IPR002313. Lys-tRNA-ligase_II.
IPR018149. Lys-tRNA-synth_II_C.
IPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
IPR031553. tRNA-synt_2_TM.
[Graphical view]
PANTHERiPTHR22594. PTHR22594. 1 hit.
PfamiPF09924. DUF2156. 1 hit.
PF00152. tRNA-synt_2. 1 hit.
PF16995. tRNA-synt_2_TM. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view]
PRINTSiPR00982. TRNASYNTHLYS.
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00499. lysS_bact. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C., Fraser C.M.
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  2. "Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
    Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
    Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  3. "Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
    Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
    Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.

Entry informationi

Entry nameiLYSX_MYCS2
AccessioniPrimary (citable) accession number: A0QYV1
Secondary accession number(s): I7GAI7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 18, 2010
Last sequence update: May 18, 2010
Last modified: May 11, 2016
This is version 81 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.