RegulonDB RegulonDB 10.10: Gene Form
   

lysS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lysS prfB idi TSS_3164 TSS_3164 TSS_3163 TSS_3163 TSS_3162 (cluster) TSS_3162 (cluster) TSS_3161 TSS_3161 TSS_3160 TSS_3160 TSS_3159 TSS_3159 TSS_3158 TSS_3158 TSS_3157 TSS_3157 TSS_3156 TSS_3156 TSS_3155 TSS_3155 TSS_3154 TSS_3154 TSS_3153 TSS_3153 TSS_3152 TSS_3152 TSS_3151 TSS_3151 TSS_3150 TSS_3150 TSS_3149 TSS_3149 TSS_3148 TSS_3148 TSS_3147 TSS_3147 TSS_3146 TSS_3146

Gene      
Name: lysS    Texpresso search in the literature
Synonym(s): ECK2885, EG10552, asuD, b2890, herC
Genome position(nucleotides): 3033657 <-- 3035174 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.1
External database links:  
ASAP:
 ABE-0009486
CGSC:
 17662
ECHOBASE:
 EB0547
ECOLIHUB:
 lysS
OU-MICROARRAY:
 b2890
STRING:
 511145.b2890
COLOMBOS: lysS


Product      
Name: lysine—tRNA ligase, constitutive
Synonym(s): AsuD, HerC, LysRSs, LysS
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,membrane
Molecular weight: 57.603
Isoelectric point: 4.876
Motif(s):
 
Type Positions Sequence
68 -> 146 VAVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDDLPEGVYNEQFKKWDLGDILGAKGKLFKTKTGELSIHCTELRLL
2 -> 505 SEQHAQGADAVVDLNNELKTRREKLANLREQGIAFPNDFRRDHTSDQLHAEFDGKENEELEALNIEVAVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDDLPEGVYNEQFKKWDLGDILGAKGKLFKTKTGELSIHCTELRLLTKALRPLPDKFHGLQDQEARYRQRYLDLISNDESRNTFKVRSQILSGIRQFMVNRGFMEVETPMMQVIPGGAAARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYKDLIELTESLFRTLAQDILGKTEVTYGDVTLDFGKPFEKLTMREAIKKYRPETDMADLDNFDSAKAIAESIGIHVEKSWGLGRIVTEIFEEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAQRFLDQVAAKDAGDDEAMFYDEDYVTALEHGLPPTAGLGIGIDRMVMLFTNSHTIRDVILFPAMRPVK
162 -> 501 DQEARYRQRYLDLISNDESRNTFKVRSQILSGIRQFMVNRGFMEVETPMMQVIPGGAAARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYKDLIELTESLFRTLAQDILGKTEVTYGDVTLDFGKPFEKLTMREAIKKYRPETDMADLDNFDSAKAIAESIGIHVEKSWGLGRIVTEIFEEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAQRFLDQVAAKDAGDDEAMFYDEDYVTALEHGLPPTAGLGIGIDRMVMLFTNSHTIRDVILFPAM

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.1 - amino acid -activation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
molecular_function GO:0003676 - nucleic acid binding
GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016874 - ligase activity
GO:0004812 - aminoacyl-tRNA ligase activity
GO:0004824 - lysine-tRNA ligase activity
GO:0000049 - tRNA binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0000287 - magnesium ion binding
GO:0042803 - protein homodimerization activity
biological_process GO:0006412 - translation
GO:0006418 - tRNA aminoacylation for protein translation
GO:0006430 - lysyl-tRNA aminoacylation
Note(s): Note(s): ...[more].
Reference(s): [1] Airas RK. 2007
[2] Alexandrescu AT., et al., 1999
[3] Alexandrescu AT., et al., 2000
[4] Boy E., et al., 1978
[5] Boy E., et al., 1976
[6] Brevet A., et al., 1989
[7] Buttcher V., et al., 1994
[8] Clark RL., et al., 1990
[9] Despotovic D., et al., 2017
[10] Dittgen RM., et al., 1976
[11] Emmerich RV., et al., 1987
[12] Fukunaga J., et al., 2006
[13] Gampel A., et al., 1989
[14] Hassani M., et al., 1991
[15] Hirshfield IN., et al., 1977
[16] Hirshfield IN., et al., 1984
[17] Hirshfield IN., et al., 1972
[18] Hirshfield IN., et al., 1976
[19] Hirshfield IN., et al., 1975
[20] Hirshfield IN., et al., 1976
[21] Hirshfield IN., et al., 1972
[22] Kawakami K., et al., 1989
[23] Kim CW., et al., 2007
[24] McBroom AJ., et al., 2006
[25] Mirande M. 1991
[26] Neidhardt FC., et al., 1977
[27] Reinisch F., et al., 1975
[28] Saluta MV., et al., 1995
[29] Sullivan MA., et al., 1985
External database links:  
DIP:
 DIP-36211N
ECOCYC:
 LYSS-MONOMER
ECOLIWIKI:
 b2890
INTERPRO:
 IPR034762
INTERPRO:
 IPR018149
INTERPRO:
 IPR012340
INTERPRO:
 IPR006195
INTERPRO:
 IPR004365
INTERPRO:
 IPR004364
INTERPRO:
 IPR002313
PDB:
 1KRT
PDB:
 1BBU
PDB:
 1BBW
PDB:
 1KRS
PFAM:
 PF01336
PFAM:
 PF00152
PRIDE:
 P0A8N3
PRINTS:
 PR00982
PROSITE:
 PS50862
REFSEQ:
 NP_417366
SMR:
 P0A8N3
UNIPROT:
 P0A8N3


Operon      
Name: xerD-dsbC-recJ-prfB-lysS         
Operon arrangement:
Transcription unit        Promoter
dsbC
dsbC-recJ-prfB
xerD-dsbC-recJ
xerD-dsbC-recJ
prfB-lysS
xerD


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_3146 3034170 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3147 3034200 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3148 3034309 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3149 3034602 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3150 3034638 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3151 3034998 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3152 3035019 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3153 3035030 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3154 3035058 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3155 3035062 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3156 3035121 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3157 3035166 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3158 3035202 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3159 3035315 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3160 3035434 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3161 3036095 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3162 (cluster) 3036210 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3163 3036221 reverse nd [RS-EPT-CBR] [30]
  promoter TSS_3164 3036252 reverse nd [RS-EPT-CBR] [30]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Airas RK., 2007, Magnesium dependence of the measured equilibrium constants of aminoacyl-tRNA synthetases., Biophys Chem 131(1-3):29-35

 [2] Alexandrescu AT., Jaravine VA., Dames SA., Lamour FP., 1999, NMR hydrogen exchange of the OB-fold protein LysN as a function of denaturant: the most conserved elements of structure are the most stable to unfolding., J Mol Biol 289(4):1041-54

 [3] Alexandrescu AT., Lamour FP., Jaravine VA., 2000, NMR evidence for progressive stabilization of native-like structure upon aggregation of acid-denatured LysN., J Mol Biol 295(2):239-55

 [4] Boy E., Borne F., Patte JC., 1978, Effect of mutations affecting lysyl-tRNAlys on the regulation of lysine biosynthesis in Escherichia coli., Mol Gen Genet 159(1):33-8

 [5] Boy E., Reinisch F., Richaud C., Patte JC., 1976, Role of lysyl-tRNA in the regulation of lysine biosynthesis in Escherichia coli K12., Biochimie 58(1-2):213-8

 [6] Brevet A., Chen J., Leveque F., Plateau P., Blanquet S., 1989, In vivo synthesis of adenylylated bis(5'-nucleosidyl) tetraphosphates (Ap4N) by Escherichia coli aminoacyl-tRNA synthetases., Proc Natl Acad Sci U S A 86(21):8275-9

 [7] Buttcher V., Senger B., Schumacher S., Reinbolt J., Fasiolo F., 1994, Modulation of the suppression efficiency and amino acid identity of an artificial yeast amber isoleucine transfer RNA in Escherichia coli by a G-U pair in the anticodon stem., Biochem Biophys Res Commun 200(1):370-7

 [8] Clark RL., Neidhardt FC., 1990, Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior., J Bacteriol 172(6):3237-43

 [9] Despotovic D., Brandis A., Savidor A., Levin Y., Fumagalli L., Tawfik DS., 2017, Diadenosine tetraphosphate (Ap4A) - an E. coli alarmone or a damage metabolite?, FEBS J 284(14):2194-2215

 [10] Dittgen RM., Leberman R., 1976, Multiple forms of lysyl-tRNA synthetase from Escherichia coli., Hoppe Seylers Z Physiol Chem 357(4):543-51

 [11] Emmerich RV., Hirshfield IN., 1987, Mapping of the constitutive lysyl-tRNA synthetase gene of Escherichia coli K-12., J Bacteriol 169(11):5311-3

 [12] Fukunaga J., Yokogawa T., Ohno S., Nishikawa K., 2006, Misacylation of yeast amber suppressor tRNA(Tyr) by E. coli lysyl-tRNA synthetase and its effective repression by genetic engineering of the tRNA sequence., J Biochem 139(4):689-96

 [13] Gampel A., Tzagoloff A., 1989, Homology of aspartyl- and lysyl-tRNA synthetases., Proc Natl Acad Sci U S A 86(16):6023-7

 [14] Hassani M., Saluta MV., Bennett GN., Hirshfield IN., 1991, Partial characterization of a lysU mutant of Escherichia coli K-12., J Bacteriol 173(6):1965-70

 [15] Hirshfield IN., Liu C., Yeh FM., 1977, Two modes of metabolic regulation of lysyl-transfer ribonucleic acid synthetase in Escherichia coli K-12., J Bacteriol 131(2):589-97

 [16] Hirshfield IN., Tenreiro R., Vanbogelen RA., Neidhardt FC., 1984, Escherichia coli K-12 lysyl-tRNA synthetase mutant with a novel reversion pattern., J Bacteriol 158(2):615-20

 [17] Hirshfield IN., Tomford JW., Zamecnik PC., 1972, Thiosine-resistant mutants of Escherichia coli K-12 with growth-medium-dependent lysyl-tRNA synthetase activity.II. Evidence for an altered lysyl-tRNA synthetase., Biochim Biophys Acta 259(3):344-56

 [18] Hirshfield IN., Yeh FM., 1976, An in vivo effect of the metabolites L-alanine and glycyl-L-leucine on the properties of the lysyl-tRNA synthetase from Escherichia coli K-12. II. Kinetic evidence., Biochim Biophys Acta 435(3):306-14

 [19] Hirshfield IN., Yeh FM., Sawyer LE., 1975, Metabolites influence control of lysine transfer ribonucleic acid synthetase formation in Escherichia coli K-12., Proc Natl Acad Sci U S A 72(4):1364-7

 [20] Hirshfield IN., Yeh FM., Zamecnik PC., 1976, An in vivo effect of the metabolites L-alanine and glycyl-L-leucine on the properties of lysyl-tRNA synthetase from Escherichia coli K-12. I. Influence on subunit composition and molecular weight distribution., Biochim Biophys Acta 435(3):290-305

 [21] Hirshfield IN., Zamecnik PC., 1972, Thiosine-resistant mutants of Escherichia coli K-12 with growth-medium-dependent lysl-tRNA synthetase activity. I. Isolation and physiological characterization., Biochim Biophys Acta 259(3):330-43

 [22] Kawakami K., Naito S., Inoue N., Nakamura Y., Ikeda H., Uchida H., 1989, Isolation and characterization of herC, a mutation of Escherichia coli affecting maintenance of ColE1., Mol Gen Genet 219(3):333-40

 [23] Kim CW., Han KS., Ryu KS., Kim BH., Kim KH., Choi SI., Seong BL., 2007, N-terminal domains of native multidomain proteins have the potential to assist de novo folding of their downstream domains in vivo by acting as solubility enhancers., Protein Sci 16(4):635-43

 [24] McBroom AJ., Johnson AP., Vemulapalli S., Kuehn MJ., 2006, Outer membrane vesicle production by Escherichia coli is independent of membrane instability., J Bacteriol 188(15):5385-92

 [25] Mirande M., 1991, Aminoacyl-tRNA synthetases and DNA replication. Molecular mimicry between RNAII and tRNA(Lys)., FEBS Lett 283(1):1-3

 [26] Neidhardt FC., Bloch PL., Pedersen S., Reeh S., 1977, Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli., J Bacteriol 129(1):378-87

 [27] Reinisch F., Boy E., Patte JC., 1975, [Regulation of lysyl-tRNA synthetase of Escherichia coli K12]., C R Acad Sci Hebd Seances Acad Sci D 280(17):2041-3

 [28] Saluta MV., Hirshfield IN., 1995, The occurrence of duplicate lysyl-tRNA synthetase gene homologs in Escherichia coli and other procaryotes., J Bacteriol 177(7):1872-8

 [29] Sullivan MA., Cannon JF., Webb FH., Bock RM., 1985, Antisuppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2-thiouridine., J Bacteriol 161(1):368-76

 [30] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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