InterPro : IPR002313

Name  Lysine-tRNA ligase, class II Short Name  Lys-tRNA-ligase_II
Type  Family 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 []. 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 [].The aminoacyl-tRNA synthetase (also known as aminoacyl-tRNA ligase) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. 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 []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-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 and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine 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.
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Sequence Features

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Proteins

InterPro protein domain ID --> Contigs

 

Other

0 Child Features

5 Contains

Id Name Short Name Type
IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N) aa-tRNA-synt_II Domain
IPR012340 Nucleic acid-binding, OB-fold NA-bd_OB-fold Domain
IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type NA-bd_OB_tRNA Domain
IPR006195 Aminoacyl-tRNA synthetase, class II aa-tRNA-synth_II Domain
IPR018149 Lysyl-tRNA synthetase, class II, C-terminal Lys-tRNA-synth_II_C Domain

0 Found In

1 Parent Features

Id Name Short Name Type
IPR018150 Aminoacyl-tRNA synthetase, class II (D/K/N)-like aa-tRNA-synt_II-like Family

8 Publications

First Author Title Year Journal Volume Pages
Perona JJ Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. 1993 Biochemistry 32 8758-71
Delarue M The aminoacyl-tRNA synthetase family: modules at work. 1993 Bioessays 15 675-87
Cusack S Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. 1991 Nucleic Acids Res 19 3489-98
Schimmel P Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code. 1991 Trends Biochem Sci 16 1-3
Sugiura I The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. 2000 Structure 8 197-208
Eriani G Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. 1990 Nature 347 203-6
Ibba M A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. 1997 Science 278 1119-22
Desogus G Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction. 2000 Biochemistry 39 8418-25



To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)