Serine-tRNA ligase type 2, archaea (IPR004503)

Short name: Ser-tRNA-ligase_2_arc

Overlapping homologous superfamilies


Family relationships



Serine-tRNA ligase (EC: exists as monomer and belongs to class IIa [PMID: 7540217]. The serine-tRNA ligases from a few of the archaea that belong to this group are different from the set of mutually more closely related serine-tRNA ligases from eubacteria, eukaryotes, and other archaea (IPR002317).

There are two distinct types of seryl-tRNA synthetase, as differentiated by primary sequence analysis, three-dimensional structure and substrate recognition mechanism: type 1 (IPR002317) is found in the majority of organisms (prokaryotes, eukaryotes and archaea), whereas type 2 (this entry) is confined to some methanogenic archaea [PMID: 19734148]. Methanosarcina barkeri possesses two seryl-tRNA synthetases, one of each type [PMID: 15364939].

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 [PMID: 10704480,PMID: 12458790]. These proteins differ widely in size and oligomeric state, and have limited sequence homology [PMID: 2203971]. 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 [PMID: 10673435]. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [PMID: 8364025], and are mostly dimeric or multimeric, containing at least three conserved regions [PMID: 8274143, PMID: 2053131, PMID: 1852601]. 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, 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 [PMID: 10447505].

GO terms

Biological Process

GO:0006434 seryl-tRNA aminoacylation

Molecular Function

GO:0005524 ATP binding
GO:0000166 nucleotide binding
GO:0004828 serine-tRNA ligase activity

Cellular Component

GO:0005737 cytoplasm

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.