Family

Glycine-tRNA ligase, archaeal (IPR022960)

Short name: Gly_tRNA_ligase_arc

Family relationships

Description

This entry represents archaeal glycine-tRNA ligases (also known as glycyl-tRNA synthetases).

In eubacteria, glycine-tRNA ligase(EC:6.1.1.14) is an alpha2/beta2 tetramer composed of 2 different subunits [PMID: 6309809, PMID: 7962006, PMID: 7665503]. In some eubacteria, in archaea and eukaryota, glycine-tRNA ligase is an alpha2 dimer, this family. It belongs to class IIc and is one of the most complex ligases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310) and beta subunits (see IPR002311) also lack significant sequence similarity. However, they are translated from a single mRNA [PMID: 6309809], and a single chain glycine-tRNA ligase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain [PMID: 7665503].

The sequence and crystal structure of the homodimeric glyccine-tRNA ligase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA ligase due to the conserved nature of the class II active site [PMID: 7556056, PMID: 10064708].

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 [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 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.

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0004820 glycine-tRNA ligase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

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