F
IPR002313

Lysine-tRNA ligase, class II

InterPro entry
Short nameLys-tRNA-ligase_II
Overlapping
homologous
superfamilies
 
family relationships

Description

This entry represents lysine-tRNA ligase class II.

Lysine-tRNA synthesis is catalysed by two unrelated families of tRNA ligases: class-I or class-II. In eubacteria and eukaryota lysine-tRNA ligases belong to class II, the same family as aspartyl tRNA ligase. The lysine-tRNA ligase class Ic family is present in archaea and some eubacteria
[7]
. Moreover in some eubacteria there is a gene X, which is similar to a part of lysine-tRNA ligase from class II.

Lysine-tRNA ligase is duplicated in some species with, for example in Escherichia coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding
[11]
.

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction
[4, 3]
. These proteins differ widely in size and oligomeric state, and have limited sequence homology
[8]
. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric
[6]
. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices
[2]
, and are mostly dimeric or multimeric, containing at least three conserved regions
[10, 9, 1]
. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c
[5]
.

References

1.Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Cusack S, Hartlein M, Leberman R. Nucleic Acids Res. 19, 3489-98, (1991). View articlePMID: 1852601

2.Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Perona JJ, Rould MA, Steitz TA. Biochemistry 32, 8758-71, (1993). View articlePMID: 8364025

3.Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. Francklyn C, Perona JJ, Puetz J, Hou YM. RNA 8, 1363-72, (2002). View articlePMID: 12458790

4.Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Woese CR, Olsen GJ, Ibba M, Soll D. Microbiol. Mol. Biol. Rev. 64, 202-36, (2000). View articlePMID: 10704480

5.Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV. Genome Res. 9, 689-710, (1999). View articlePMID: 10447505

6.The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. Sugiura I, Nureki O, Ugaji-Yoshikawa Y, Kuwabara S, Shimada A, Tateno M, Lorber B, Giege R, Moras D, Yokoyama S, Konno M. Structure 8, 197-208, (2000). View articlePMID: 10673435

7.A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, Soll D. Science 278, 1119-22, (1997). View articlePMID: 9353192

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

9.Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code. Schimmel P. Trends Biochem. Sci. 16, 1-3, (1991). View articlePMID: 2053131

10.The aminoacyl-tRNA synthetase family: modules at work. Delarue M, Moras D. Bioessays 15, 675-87, (1993). View articlePMID: 8274143

11.Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction. Desogus G, Todone F, Brick P, Onesti S. Biochemistry 39, 8418-25, (2000). View articlePMID: 10913247

GO terms

Cross References

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