Escherichia coli K-12 substr. MG1655 Enzyme: Ap3A synthetase / Ap4A synthetase / lysyl-tRNA synthetase

Gene: lysU Accession Numbers: EG10553 (EcoCyc), b4129, ECK4123

Regulation Summary Diagram: ?

Regulation summary diagram for lysU

Subunit composition of Ap3A synthetase / Ap4A synthetase / lysyl-tRNA synthetase = [LysU]2
         lysyl-tRNA synthetase = LysU

The lysyl-tRNA synthetase LysU is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. LysU belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology [Eriani90, Cusack91]. E. coli contains both a constitutive and an inducible lysyl-tRNA synthetase; lysU encodes the inducible enzyme [Hirshfield81, VanBogelen83].

LysU catalyzes misacylation of tRNALys with arginine, threonine, methionine, leucine, alanine, serine, and cysteine, although the most efficient noncognate substrate, arginine, is used with 1600-fold lower catalytic efficiency than the cognate amino acid lysine [Jakubowski99]. The enzyme does not appear to possess a post-transfer editing mechanism, but it does possesses an efficient pre-transfer editing function, discriminating against ornithine [Jakubowski99]. LysU edits homocysteine, homoserine and ornithine by a cyclization mechanism [Jakubowski97, Jakubowski99].

LysU catalyzes the formation of diadenosine tetra- and triphosphate (Ap4A, Ap3A) both in vitro and in vivo [Plateau82, Charlier87, Brevet89]. Both the tRNA charging reaction and the synthesis of Ap4A and Ap3A share a common lysyl-adenylate intermediate; the subsequent formation of Ap4A in the presence of Zn2+ and ATP is reversible and allows the later appearance of Ap3A in the presence of Zn2+ and ADP [Wright06].

LysU can adenylate HinT in the presence of Mg2+ and lysine, indicating a dependence on the formation of the lysyl-AMP intermediate; the reaction is inhibited by Zn2+, Ap4A and Ap3A and enhanced by the presence of pyrophosphatase [Chou07].

A phosphorylated form of LysU containing a single phosphothreonine residue can be isolated; it does not show significant differences in catalytic activity, but may be more stable than the nonphosphorylated form [Wright06].

LysU may [Clark90] or may not [Hassani91] be required for normal growth at elevated temperature. lysU expression is induced by elevated temperature, anaerobiosis, and low pH [Hickey90, Charlier87, Leveque91, Hassani92]. LysU is negatively regulated by H-NS [Ito94] and is a member of the Lrp (leucine-responsive regulatory protein) regulon [Ernsting92, Gazeau92, Lin92, Ito93]. Cooperative binding of Lrp to the lysU promoter region represses transcription [Gazeau94]. Overexpression of lysU suppresses the low temperature growth defect of a lysS null mutant [Kawakami92].

The enzyme is a homodimer [Onesti95]. Crystal structures of LysU are presented [Onesti95, Desogus00]. Biochemical and computational molecular dynamics studies of the reaction mechanism have been performed [Hughes03, Hughes06].

Reviews: [Nakamura93, Freist95]
ArcA appears to activate lysU gene expression under anaerobiosis. A putative ArcA binding site was identified 201 bp upstream of this gene [Salmon05]; but it is not known which of the two promoters transcribing the gene is affected.

Gene Citations: [Oshima95]

Locations: cytosol, membrane

Map Position: [4,351,223 <- 4,352,740] (93.78 centisomes, 338°)
Length: 1518 bp / 505 aa

Molecular Weight of Polypeptide: 57.827 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013520 , CGSC:16693 , DIP:DIP-36212N , EchoBASE:EB0548 , EcoGene:EG10553 , EcoliWiki:b4129 , Mint:MINT-1219496 , OU-Microarray:b4129 , PortEco:lysU , PR:PRO_000023141 , Pride:P0A8N5 , Protein Model Portal:P0A8N5 , RefSeq:NP_418553 , RegulonDB:EG10553 , SMR:P0A8N5 , String:511145.b4129 , UniProt:P0A8N5

Relationship Links: InterPro:IN-FAMILY:IPR002313 , InterPro:IN-FAMILY:IPR004364 , InterPro:IN-FAMILY:IPR004365 , InterPro:IN-FAMILY:IPR006195 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR018149 , InterPro:IN-FAMILY:IPR018150 , Panther:IN-FAMILY:PTHR22594 , PDB:Structure:1E1O , PDB:Structure:1E1T , PDB:Structure:1E22 , PDB:Structure:1E24 , PDB:Structure:1LYL , Pfam:IN-FAMILY:PF00152 , Pfam:IN-FAMILY:PF01336 , Prints:IN-FAMILY:PR00982 , Prosite:IN-FAMILY:PS50862

In Paralogous Gene Group: 225 (4 members) , 575 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Instance reaction of [an acyl-carrier protein + coenzyme A → adenosine 3',5'-bisphosphate + a holo-[acyl-carrier protein] + H+] (
i1: [EntB aryl-carrier protein] + coenzyme A → a holo EntB isochorismatase/aryl-carrier protein + adenosine 3',5'-bisphosphate + H+ (

Genetic Regulation Schematic: ?

Genetic regulation schematic for lysU

GO Terms:

Biological Process: GO:0006418 - tRNA aminoacylation for protein translation Inferred from experiment Inferred by computational analysis [GOA01a, Brevet95]
GO:0006430 - lysyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Brevet95]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA06, Desogus00]
GO:0004824 - lysine-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Brevet95]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Desogus00]
GO:0016874 - ligase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Brevet95]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for lysU knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Last-Curated ? 20-Dec-2006 by Keseler I , SRI International

Enzymatic reaction of: Ap3A synthetase

EC Number: 2.7.7.-

ATP + ADP + H+ <=> 5',5'''-diadenosine triphosphate + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: L-lysine

Activators (Unknown Mechanism): Zn2+ [Plateau82]

Enzymatic reaction of: Ap4A synthetase

EC Number: 2.7.7.-

ATP + ATP + H+ <=> 5',5'''-diadenosine tetraphosphate + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

Cofactors or Prosthetic Groups: L-lysine

Activators (Unknown Mechanism): Zn2+ [Plateau82, Charlier87]

T(opt): 46 °C [Charlier87]

pH(opt): 7.6 [Charlier87]

Enzymatic reaction of: lysyl-tRNA synthetase

Synonyms: LysRSu

EC Number:

L-lysine + a tRNAlys + ATP + H+ <=> an L-lysyl-[tRNAlys] + AMP + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA charging

Cofactors or Prosthetic Groups: Mg2+ [Charlier87]

Inhibitors (Unknown Mechanism): Zn2+ [Plateau82, Charlier87]

Kinetic Parameters:

Km (μM)
a tRNAlys

T(opt): 35 °C [Charlier87]

pH(opt): 8.3 [Charlier87]

Sequence Features

Protein sequence of lysyl-tRNA synthetase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Leveque90, UniProt11]
UniProt: Removed.
Chain 2 -> 505
UniProt: Lysyl-tRNA synthetase, heat inducible;
N6-acetyllysine-Modification 114
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Sequence-Conflict 125
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
N6-acetyllysine-Modification 156
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Sequence-Conflict 236
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
Sequence-Conflict 258 -> 262
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
Sequence-Conflict 268 -> 269
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
Sequence-Conflict 351
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
Sequence-Conflict 371
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
Sequence-Conflict 380 -> 384
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
Sequence-Conflict 388
[Clark90, UniProt10a]
UniProt: (in Ref. 3; AAA24096);
Metal-Binding-Site 415
UniProt: Magnesium 1.
Metal-Binding-Site 422
UniProt: Magnesium 1.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4129 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10553; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Brevet89: 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. PMID: 2554306

Brevet95: Brevet A, Chen J, Leveque F, Blanquet S, Plateau P (1995). "Comparison of the enzymatic properties of the two Escherichia coli lysyl-tRNA synthetase species." J Biol Chem 270(24);14439-44. PMID: 7782306

Charlier87: Charlier J, Sanchez R (1987). "Lysyl-tRNA synthetase from Escherichia coli K12. Chromatographic heterogeneity and the lysU-gene product." Biochem J 248(1);43-51. PMID: 3325036

Chou07: Chou TF, Wagner CR (2007). "Lysyl-tRNA synthetase generated lysyl-adenylate is a substrate for histidine triad nucleotide binding proteins." J Biol Chem 282(7):4719-27. PMID: 17158446

Clark90: 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. PMID: 2188953

Cusack91: Cusack S, Hartlein M, Leberman R (1991). "Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases." Nucleic Acids Res 19(13);3489-98. PMID: 1852601

Desogus00: Desogus G, Todone F, Brick P, Onesti S (2000). "Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction." Biochemistry 39(29);8418-25. PMID: 10913247

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Eriani90: Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs." Nature 347(6289);203-6. PMID: 2203971

Ernsting92: Ernsting BR, Atkinson MR, Ninfa AJ, Matthews RG (1992). "Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli." J Bacteriol 174(4);1109-18. PMID: 1346534

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Freist95: Freist W, Gauss DH (1995). "Lysyl-tRNA synthetase." Biol Chem Hoppe Seyler 376(8);451-72. PMID: 7576245

Gazeau92: Gazeau M, Delort F, Dessen P, Blanquet S, Plateau P (1992). "Escherichia coli leucine-responsive regulatory protein (Lrp) controls lysyl-tRNA synthetase expression." FEBS Lett 300(3);254-8. PMID: 1555652

Gazeau94: Gazeau M, Delort F, Fromant M, Dessen P, Blanquet S, Plateau P (1994). "Structure-function relationship of the Lrp-binding region upstream of lysU in Escherichia coli." J Mol Biol 241(3);378-89. PMID: 8064854

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hassani91: 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. PMID: 2001999

Hassani92: Hassani M, Pincus DH, Bennett GN, Hirshfield IN (1992). "Temperature-dependent induction of an acid-inducible stimulon of Escherichia coli in broth." Appl Environ Microbiol 58(8);2704-7. PMID: 1514820

Hickey90: Hickey EW, Hirshfield IN (1990). "Low-pH-induced effects on patterns of protein synthesis and on internal pH in Escherichia coli and Salmonella typhimurium." Appl Environ Microbiol 56(4);1038-45. PMID: 2187401

Hirshfield81: Hirshfield IN, Bloch PL, Van Bogelen RA, Neidhardt FC (1981). "Multiple forms of lysyl-transfer ribonucleic acid synthetase in Escherichia coli." J Bacteriol 146(1);345-51. PMID: 7012120

Hughes03: Hughes SJ, Tanner JA, Hindley AD, Miller AD, Gould IR (2003). "Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment." BMC Struct Biol 3(1);5. PMID: 12787471

Hughes06: Hughes SJ, Tanner JA, Miller AD, Gould IR (2006). "Molecular dynamics simulations of LysRS: an asymmetric state." Proteins 62(3);649-62. PMID: 16317719

Ibba00: Ibba M, Soll D (2000). "Aminoacyl-tRNA synthesis." Annu Rev Biochem 69;617-50. PMID: 10966471

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Ito93: Ito K, Kawakami K, Nakamura Y (1993). "Multiple control of Escherichia coli lysyl-tRNA synthetase expression involves a transcriptional repressor and a translational enhancer element." Proc Natl Acad Sci U S A 90(1);302-6. PMID: 7678344

Ito94: Ito K, Oshima T, Mizuno T, Nakamura Y (1994). "Regulation of lysyl-tRNA synthetase expression by histone-like protein H-NS of Escherichia coli." J Bacteriol 176(23);7383-6. PMID: 7961513

Jakubowski97: Jakubowski H (1997). "Aminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases." Biochemistry 36(37);11077-85. PMID: 9287150

Jakubowski99: Jakubowski H (1999). "Misacylation of tRNALys with noncognate amino acids by lysyl-tRNA synthetase." Biochemistry 38(25);8088-93. PMID: 10387054

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kawakami92: Kawakami K, Ito K, Nakamura Y (1992). "Differential regulation of two genes encoding lysyl-tRNA synthetases in Escherichia coli: lysU-constitutive mutations compensate for a lysS null mutation." Mol Microbiol 6(13);1739-45. PMID: 1321323

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Leveque90: 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 1990;18(2);305-12. PMID: 2183178

Leveque91: Leveque F, Gazeau M, Fromant M, Blanquet S, Plateau P (1991). "Control of Escherichia coli lysyl-tRNA synthetase expression by anaerobiosis." J Bacteriol 173(24);7903-10. PMID: 1744045

Lin92: Lin R, Ernsting B, Hirshfield IN, Matthews RG, Neidhardt FC, Clark RL, Newman EB (1992). "The lrp gene product regulates expression of lysU in Escherichia coli K-12." J Bacteriol 174(9);2779-84. PMID: 1569010

Nakamura93: Nakamura Y, Ito K (1993). "Control and function of lysyl-tRNA synthetases: diversity and co-ordination." Mol Microbiol 10(2);225-31. PMID: 7934813

Onesti95: Onesti S, Miller AD, Brick P (1995). "The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli." Structure 3(2);163-76. PMID: 7735833

Oshima95: Oshima T, Ito K, Kabayama H, Nakamura Y (1995). "Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp." Mol Gen Genet 1995;247(5);521-8. PMID: 7603430

Plateau82: 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. PMID: 6756470

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

VanBogelen83: VanBogelen RA, Vaughn V, Neidhardt FC (1983). "Gene for heat-inducible lysyl-tRNA synthetase (lysU) maps near cadA in Escherichia coli." J Bacteriol 153(2);1066-8. PMID: 6337114

Wright06: Wright M, Boonyalai N, Tanner JA, Hindley AD, Miller AD (2006). "The duality of LysU, a catalyst for both Ap4A and Ap3A formation." FEBS J 273(15);3534-44. PMID: 16884494

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Fraenkel95: Fraenkel YM, Mandel Y, Friedberg D, Margalit H (1995). "Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon." Comput Appl Biosci 1995;11(4);379-87. PMID: 8521047

Lin92a: Lin R, D'Ari R, Newman EB (1992). "Lambda placMu insertions in genes of the leucine regulon: extension of the regulon to genes not regulated by leucine." J Bacteriol 1992;174(6);1948-55. PMID: 1532173

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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