Escherichia coli K-12 substr. MG1655 Enzyme: lysyl-tRNA synthetase, constitutive

Gene: lysS Accession Numbers: EG10552 (EcoCyc), b2890, ECK2885

Synonyms: asuD, herC

Regulation Summary Diagram: ?

Regulation summary diagram for lysS

Subunit composition of lysyl-tRNA synthetase, constitutive = [LysS]2
         lysyl tRNA synthetase (LysRSs), constitutive = LysS

The lysyl-tRNA synthetase LysS 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. LysS belongs to the subclass IIb of aminoacyl tRNA synthetases. E. coli contains both a constitutive and an inducible lysyl tRNA synthetase; lysS encodes the constitutively expressed enzyme.

Key residues for recognition of the cognate amino acid and catalytic activity have been identified [Ataide04], providing insight into differences between the class I and class II tRNA synthetases. A model for the recognition specificity of the cognate anticodon is presented [Commans98].

Under aerobic conditions and at growth temperatures below 37 degrees C, LysS is required for normal growth [Leveque91]; the growth defect can be suppressed by overexpression of lysU, the gene encoding the inducible lysyl tRNA synthetase [Kawakami92].

Solution structures [Commans95] and a crystal structure [Onesti00] of LysS are presented, revealing reorganization of the active site upon lysine binding.

Reviews: [Nakamura93, Freist95]

Gene Citations: [Kawakami88a, Leveque90]

Locations: cytosol, membrane

Map Position: [3,031,679 <- 3,033,196] (65.34 centisomes, 235°)
Length: 1518 bp / 505 aa

Molecular Weight of Polypeptide: 57.603 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009486 , CGSC:17662 , DIP:DIP-36211N , EchoBASE:EB0547 , EcoGene:EG10552 , EcoliWiki:b2890 , Mint:MINT-1227180 , OU-Microarray:b2890 , PortEco:lysS , Pride:P0A8N3 , Protein Model Portal:P0A8N3 , RefSeq:NP_417366 , RegulonDB:EG10552 , SMR:P0A8N3 , String:511145.b2890 , UniProt:P0A8N3

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:1BBU , PDB:Structure:1BBW , PDB:Structure:1KRS , PDB:Structure:1KRT , 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 lysS

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:0004824 - lysine-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Brevet95]
GO:0016874 - ligase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Brevet95]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, 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 lysS knockouts: ?

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

Enzymatic reaction of: lysyl-tRNA synthetase

Synonyms: LysRSs

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

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Baturina72, BRENDA14]
5.0, 6.0
[Kisselev72, BRENDA14]
[Hele72, BRENDA14]
[Jakubowski99, BRENDA14]
[Ataide04, BRENDA14]
37.0, 330.0
[Kisselev72, BRENDA14]
[Ataide04, BRENDA14]
a tRNAlys
2.0, 5.7
[Kisselev72, BRENDA14]
a tRNAlys

Sequence Features

Protein sequence of lysyl tRNA synthetase (LysRSs), constitutive with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Leveque90, UniProt11]
UniProt: Removed.
Chain 2 -> 505
UniProt: Lysyl-tRNA synthetase;
Metal-Binding-Site 415
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 422
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2890 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10552; confirmed by SwissProt match.


Ataide04: Ataide SF, Ibba M (2004). "Discrimination of cognate and noncognate substrates at the active site of class II lysyl-tRNA synthetase." Biochemistry 43(37);11836-41. PMID: 15362869

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

Baturina72: Baturina ID, Gnutchev NV, Khomutov RM, Kisselev LL (1972). "Substrate specificity of lysyl-tRNA synthet ase from E. coli B." FEBS Lett 22(2);235-237. PMID: 11946605

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

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

Commans95: Commans S, Plateau P, Blanquet S, Dardel F (1995). "Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys)." J Mol Biol 253(1);100-13. PMID: 7473706

Commans98: Commans S, Lazard M, Delort F, Blanquet S, Plateau P (1998). "tRNA anticodon recognition and specification within subclass IIb aminoacyl-tRNA synthetases." J Mol Biol 278(4);801-13. PMID: 9614943

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

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

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."

Hele72: Hele P, Barber R (1972). "Lysyl tRNA synthetase of Escherichia coli B: formation and reactions of ATP-enzyme and lysyl-AMP-enzyme complexes." Biochim Biophys Acta 258(1);319-31. PMID: 4333590

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

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

Kawakami88a: Kawakami K, Jonsson YH, Bjork GR, Ikeda H, Nakamura Y (1988). "Chromosomal location and structure of the operon encoding peptide-chain-release factor 2 of Escherichia coli." Proc Natl Acad Sci U S A 1988;85(15);5620-4. PMID: 2456575

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

Kisselev72: Kisselev LL, Baturina ID (1972). "Two enzymatically active forms of lysyl-tRNA synthetase from E. coli B." FEBS Lett 22(2);231-234. PMID: 11946604

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

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

Onesti00: Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P (2000). "Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding." Biochemistry 39(42);12853-61. PMID: 11041850

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Sun Oct 4, 2015, biocyc13.