Protein Domain : IPR002313

Type:  Family Name:  Lysine-tRNA ligase, class II
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. Short Name:  Lys-tRNA-ligase_II

0 Child Features

5 Contains

DB identifier Type Name
IPR012340 Domain Nucleic acid-binding, OB-fold
IPR006195 Domain Aminoacyl-tRNA synthetase, class II
IPR018149 Domain Lysyl-tRNA synthetase, class II, C-terminal
IPR004364 Domain Aminoacyl-tRNA synthetase, class II (D/K/N)
IPR004365 Domain OB-fold nucleic acid binding domain, AA-tRNA synthetase-type

3 Cross Referencess

Identifier
PIRSF039101
TIGR00499
MF_00252

0 Found In

3 GO Annotations

GO Term Gene Name Organism
GO:0004824 IPR002313
GO:0005524 IPR002313
GO:0006430 IPR002313

1 Parent Features

DB identifier Type Name
IPR018150 Family Aminoacyl-tRNA synthetase, class II (D/K/N)-like

382 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
79851 D8QXQ7 PAC:15405174 Selaginella moellendorffii 485  
272117 D8T3M2 PAC:15401427 Selaginella moellendorffii 536  
28842.m000944 B9SBP3 PAC:16801832 Ricinus communis 585  
29428.m000317 B9SY11 PAC:16802834 Ricinus communis 607  
Cucsa.152710.1 A0A0A0L1N3 PAC:16964578 Cucumis sativus 603  
Cucsa.089220.1 PAC:16957111 Cucumis sativus 689  
Cucsa.089220.2 PAC:16957112 Cucumis sativus 689  
GSVIVT01031124001 PAC:17837380 Vitis vinifera 1537  
GSVIVT01019319001 PAC:17828976 Vitis vinifera 676  
GSVIVT01025473001 D7SLL4 PAC:17833459 Vitis vinifera 592  
orange1.1g008040m A0A067ETB4 PAC:18110118 Citrus sinensis 580  
AT3G11710.1 Q9ZPI1 PAC:19662286 Arabidopsis thaliana 626  
AT3G13490.1 Q9LJE2 PAC:19662507 Arabidopsis thaliana 602  
Thhalv10020276m V4M8Z7 PAC:20181628 Eutrema salsugineum 639  
Thhalv10020313m V4M216 PAC:20181629 Eutrema salsugineum 617  
Thhalv10020319m V4M8G8 PAC:20182499 Eutrema salsugineum 610  
Thhalv10015509m V4LL92 PAC:20206530 Eutrema salsugineum 367  
Ciclev10007755m V4UK60 PAC:20794174 Citrus clementina 621  
Ciclev10014735m V4TEN7 PAC:20815462 Citrus clementina 580  
Ciclev10008055m V4UQG6 PAC:20794176 Citrus clementina 508  
Ciclev10007700m V4U153 PAC:20794173 Citrus clementina 651  
Ciclev10007757m V4UV83 PAC:20794175 Citrus clementina 620  
Carubv10013238m R0G3S4 PAC:20899485 Capsella rubella 619  
Carubv10013215m R0HK90 PAC:20899955 Capsella rubella 626  
MDP0000157382 PAC:22621900 Malus domestica 745  
MDP0000320631 PAC:22681209 Malus domestica 685  
Lus10013408 PAC:23155091 Linum usitatissimum 597  
Lus10001440 PAC:23170711 Linum usitatissimum 613  
Lus10001625 PAC:23145980 Linum usitatissimum 613  
Lus10010317 PAC:23169511 Linum usitatissimum 633  

8 Publications

First Author Title Year Journal Volume Pages PubMed ID
            8364025
            8274143
            1852601
            2053131
            10673435
            2203971
            9353192
            10913247