RegulonDB RegulonDB 10.9: Gene Form
   

lysU gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lysU dtpC ghoT Lrp terminator lysUp1 lysUp1 lysUp2 lysUp2

Gene      
Name: lysU    Texpresso search in the literature
Synonym(s): ECK4123, EG10553, b4129
Genome position(nucleotides): 4353200 <-- 4354717 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.43
External database links:  
ASAP:
ABE-0013520
CGSC:
16693
ECHOBASE:
EB0548
ECOLIHUB:
lysU
MIM:
613641
MIM:
613916
OU-MICROARRAY:
b4129
STRING:
511145.b4129
COLOMBOS: lysU


Shine dalgarno      
Sequence: agctggatttAGAGGAaccaaAAT


Product      
Name: lysine—tRNA ligase/Ap4A synthetase/Ap3A synthetase
Synonym(s): LysU
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 57.827
Isoelectric point: 4.863
Motif(s):
 
Type Positions Sequence
351 -> 351 A
162 -> 501 DQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAM
68 -> 146 VSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLL
236 -> 236 L
380 -> 384 AEAHL

 

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
molecular_function GO:0003676 - nucleic acid 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] Boonyalai N., et al., 2013
[2] Boy E., et al., 1976
[3] Chen X., et al., 2013
[4] Coste H., et al., 1987
[5] Despotovic D., et al., 2017
[6] Dittgen RM., et al., 1976
[7] Hirshfield IN., et al., 1977
[8] Hirshfield IN., et al., 1984
[9] Hirshfield IN., et al., 1972
[10] Hirshfield IN., et al., 1976
[11] Hirshfield IN., et al., 1975
[12] Hirshfield IN., et al., 1976
[13] Hirshfield IN., et al., 1972
[14] Hughes RA., et al., 2010
[15] Ji X., et al., 2019
[16] Kim JJ., et al., 1981
[17] Lagerkvist U., et al., 1977
[18] Leveque F., et al., 1990
[19] Liu Z., et al., 2015
[20] Luciano DJ., et al., 2019
[21] Matthews RG., et al., 1988
[22] Neidhardt FC., et al., 1977
[23] Onesti S., et al., 1994
[24] Plateau P., et al., 1982
[25] Plateau P., et al., 1981
[26] Prabhu NS., et al., 2017
[27] Randerath K., et al., 1966
[28] Rapaport E., et al., 1975
[29] Reinisch F., et al., 1975
[30] Rudolph B., et al., 2010
[31] Saluta MV., et al., 1995
[32] Stern R., et al., 1965
[33] Wright M., et al., 2014
[34] Wright M., et al., 2006
[35] Zamecnik PC., et al., 1966
External database links:  
DIP:
DIP-36212N
ECOCYC:
LYSU-MONOMER
ECOLIWIKI:
b4129
INTERPRO:
IPR034762
INTERPRO:
IPR018149
INTERPRO:
IPR012340
INTERPRO:
IPR006195
INTERPRO:
IPR004365
INTERPRO:
IPR004364
INTERPRO:
IPR002313
PDB:
1E1O
PDB:
1E24
PDB:
1E22
PDB:
1E1T
PDB:
1LYL
PDB:
5YZX
PFAM:
PF00152
PFAM:
PF01336
PRIDE:
P0A8N5
PRINTS:
PR00982
PRODB:
PRO_000023141
PROSITE:
PS50862
REFSEQ:
NP_418553
SMR:
P0A8N5
UNIPROT:
P0A8N5


Operon      
Name: lysU         
Operon arrangement:
Transcription unit        Promoter
lysU
lysU


Transcriptional Regulation      
Display Regulation             
Repressed by: Lrp


RNA cis-regulatory element    
Attenuation: Translational


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


Reference(s)    

 [1] Boonyalai N., Pullen JR., Abdul Wahab MF., Wright M., Miller AD., 2013, Escherichia coli LysU is a potential surrogate for human lysyl tRNA synthetase in interactions with the C-terminal domain of HIV-1 capsid protein., Org Biomol Chem 11(4):612-20

 [2] 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

 [3] Chen X., Boonyalai N., Lau C., Thipayang S., Xu Y., Wright M., Miller AD., 2013, Multiple catalytic activities of Escherichia coli lysyl-tRNA synthetase (LysU) are dissected by site-directed mutagenesis., FEBS J 280(1):102-14

 [4] Coste H., Brevet A., Plateau P., Blanquet S., 1987, Non-adenylylated bis(5'-nucleosidyl) tetraphosphates occur in Saccharomyces cerevisiae and in Escherichia coli and accumulate upon temperature shift or exposure to cadmium., J Biol Chem 262(25):12096-103

 [5] 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

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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] Hughes RA., Ellington AD., 2010, Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA., Nucleic Acids Res 38(19):6813-30

 [15] Ji X., Zou J., Peng H., Stolle AS., Xie R., Zhang H., Peng B., Mekalanos JJ., Zheng J., 2019, Alarmone Ap4A is elevated by aminoglycoside antibiotics and enhances their bactericidal activity., Proc Natl Acad Sci U S A 116(19):9578-9585

 [16] Kim JJ., Mehler AH., 1981, Stimulation of the transfer reaction of aminoacyl-tRNA synthetases by cations., Arch Biochem Biophys 209(2):465-70

 [17] Lagerkvist U., Akesson B., Branden R., 1977, Aminoacyl adenylate, a normal intermediate or a dead end in aminoacylation of transfer ribonucleic acid., J Biol Chem 252(3):1002-6

 [18] Leveque F., Plateau P., Dessen P., Blanquet S., 1990, Homology of lysS and lysU, the two Escherichia coli genes encoding distinct lysyl-tRNA synthetase species., Nucleic Acids Res 18(2):305-12

 [19] Liu Z., Vargas-Rodriguez O., Goto Y., Novoa EM., Ribas de Pouplana L., Suga H., Musier-Forsyth K., 2015, Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation., Proc Natl Acad Sci U S A 112(19):6027-32

 [20] Luciano DJ., Levenson-Palmer R., Belasco JG., 2019, Stresses that Raise Np4 A Levels Induce Protective Nucleoside Tetraphosphate Capping of Bacterial RNA., Mol Cell 75(5):957-966.e8

 [21] Matthews RG., Neidhardt FC., 1988, Abnormal induction of heat shock proteins in an Escherichia coli mutant deficient in adenosylmethionine synthetase activity., J Bacteriol 170(4):1582-8

 [22] 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

 [23] Onesti S., Theoclitou ME., Pernilla E., Wittung L., Miller AD., Plateau P., Blanquet S., Brick P., 1994, Crystallization and preliminary diffraction studies of Escherichia coli lysyl-tRNA synthetase (LysU)., J Mol Biol 243(1):123-5

 [24] Plateau P., Blanquet S., 1982, Zinc-dependent synthesis of various dinucleoside 5',5' ' '-P1,P3-Tri- or 5'',5' ' '-P1,P4-tetraphosphates by Escherichia coli lysyl-tRNA synthetase., Biochemistry 21(21):5273-9

 [25] Plateau P., Gueron M., Blanquet S., 1981, Determination of dinucleoside 5', 5"'-P1, P4- tetraphosphates by 31P and 1H NMR spectroscopy., Biochimie 63(11-12):827-30

 [26] Prabhu NS., Yun H., 2017, Comparative analysis of polyspecificity of the endogenous tRNA synthetase of different expression host towards photocrosslinking amino acids using an in silico approach., J Mol Graph Model 75:375-382

 [27] Randerath K., Janeway CM., Stephenson ML., Zamecnik PC., 1966, Isolation and characterization of dinucleoside tetra- and tri-phosphates formed in the presence of lysyl-sRNA synthetase., Biochem Biophys Res Commun 24(1):98-105

 [28] Rapaport E., Svihovec SK., Zamecnik PC., 1975, Relationship of the first step in protein synthesis to ppGpp: formation of A(5')ppp(5')Gpp., Proc Natl Acad Sci U S A 72(7):2653-7

 [29] 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

 [30] Rudolph B., Gebendorfer KM., Buchner J., Winter J., 2010, Evolution of Escherichia coli for growth at high temperatures., J Biol Chem 285(25):19029-34

 [31] 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

 [32] Stern R., Mehler AH., 1965, Lysyl-sRNA synthetase from Escherichia coli., Biochem Z 342(4):400-9

 [33] Wright M., Azhar MA., Kamal A., Miller AD., 2014, Syntheses of stable, synthetic diadenosine polyphosphate analogues using recombinant histidine-tagged lysyl tRNA synthetase (LysU)., Bioorg Med Chem Lett 24(10):2346-52

 [34] Wright M., Miller AD., 2006, Novel fluorescent labelled affinity probes for diadenosine-5',5'''-P1,P4-tetraphosphate (Ap4A)-binding studies., Bioorg Med Chem Lett 16(4):943-8

 [35] Zamecnik PC., Stephenson ML., Janeway CM., Randerath K., 1966, Enzymatic synthesis of diadenosine tetraphosphate and diadenosine triphosphate with a purified lysyl-sRNA synthetase., Biochem Biophys Res Commun 24(1):91-7


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