Protein Domain : IPR018149

Type:  Domain Name:  Lysyl-tRNA synthetase, class II, C-terminal
Description:  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.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 []. Short Name:  Lys-tRNA-synth_II_C

0 Child Features

0 Contains

1 Cross References

Identifier
PR00982

1 Found In

DB identifier Type Name
IPR002313 Family Lysine-tRNA ligase, class II

5 GO Annotations

GO Term Gene Name Organism
GO:0000166 IPR018149
GO:0004824 IPR018149
GO:0005524 IPR018149
GO:0006430 IPR018149
GO:0005737 IPR018149

1 Parent Features

DB identifier Type Name
IPR004364 Domain Aminoacyl-tRNA synthetase, class II (D/K/N)

615 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
79851 D8QXQ7 PAC:15405174 Selaginella moellendorffii 485  
140340 D8QTI9 PAC:15405936 Selaginella moellendorffii 555  
272117 D8T3M2 PAC:15401427 Selaginella moellendorffii 536  
79569 D8QXR0 PAC:15402907 Selaginella moellendorffii 287  
114752 D8SDT1 PAC:15421376 Selaginella moellendorffii 294  
428663 D8T3M1 PAC:15415590 Selaginella moellendorffii 480  
evm.model.supercontig_119.38 PAC:16406554 Carica papaya 567  
evm.model.supercontig_95.40 PAC:16428881 Carica papaya 556  
28842.m000944 B9SBP3 PAC:16801832 Ricinus communis 585  
29428.m000317 B9SY11 PAC:16802834 Ricinus communis 607  
30099.m001677 B9S7X4 PAC:16817698 Ricinus communis 668  
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  
Cucsa.298550.1 A0A0A0KT15 PAC:16975473 Cucumis sativus 670  
GSVIVT01031124001 PAC:17837380 Vitis vinifera 1537  
GSVIVT01019319001 PAC:17828976 Vitis vinifera 676  
GSVIVT01037036001 D7T3N6 PAC:17841781 Vitis vinifera 657  
GSVIVT01025473001 D7SLL4 PAC:17833459 Vitis vinifera 592  
orange1.1g048360m A0A067F0J1 PAC:18131605 Citrus sinensis 199  
orange1.1g008040m A0A067ETB4 PAC:18110118 Citrus sinensis 580  
orange1.1g043787m PAC:18129163 Citrus sinensis 452  
orange1.1g030343m A0A067DDW9 PAC:18134327 Citrus sinensis 179  
AT3G11710.1 Q9ZPI1 PAC:19662286 Arabidopsis thaliana 626  
AT4G33760.1 F4JJT9 PAC:19644208 Arabidopsis thaliana 664  
AT3G13490.1 Q9LJE2 PAC:19662507 Arabidopsis thaliana 602  
Thhalv10024609m V4MLW3 PAC:20193497 Eutrema salsugineum 668  
Thhalv10020276m V4M8Z7 PAC:20181628 Eutrema salsugineum 639  
Thhalv10020313m V4M216 PAC:20181629 Eutrema salsugineum 617  
Thhalv10020319m V4M8G8 PAC:20182499 Eutrema salsugineum 610  

8 Publications

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