Lysidine-tRNA(Ile) synthetase, N-terminal

Lysidine-tRNA(Ile) synthetase, N-terminal(InterPro Protein Domain record)

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Lysidine-tRNA(Ile) synthetase, N-terminal

InterPro Protein Domain record

description http://metadb.riken.jp/db/SciNetS_rib124i/prib124u1i

The aminoacyl-tRNA synthetases (<db_xref db="EC" dbkey="6.1.1."/>) 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 [<cite idref="PUB00007191"/>]. 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 [<cite idref="PUB00006477"/>]. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [<cite idref="PUB00000386"/>], and are mostly dimeric or multimeric, containing at least three conserved regions [<cite idref="PUB00000723"/>, <cite idref="PUB00005365"/>, <cite idref="PUB00004391"/>]. 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 [<cite idref="PUB00015156"/>]. 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.This entry represents the N-terminal domain of lysidine-tRNA(Ile) synthetase, which ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a PP-loop motif involved in ATP binding. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This domain is found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain architecture of this protein is variable; some, including characterised proteins of <taxon tax_id="562">Escherichia coli</taxon> and <taxon tax_id="1423">Bacillus subtilis</taxon> known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family. It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding [<cite idref="PUB00014303"/>]. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, E. coli NtrL, and B. subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain. The HUP domain class (after HIGH-signature proteins, UspA, and PP-ATPase) groups together PP-loop ATPases, the nucleotide-binding domains of class I aminoacyl-tRNA synthetases, UspA protein (USPA domains), photolyases, and electron transport flavoproteins (ETFP). The HUP domain is a distinct class of alpha/beta domain[<cite idref="PUB00016132"/>].More information about this protein can be found at Protein of the Month: ATP Synthases [<cite idref="PUB00020719"/>].

label http://www.w3.org/2000/01/rdf-schema#label