F
IPR012094

tRNA(Ile)-lysidine synthase

InterPro entry
Short nametRNA_Ile_lys_synt
Overlapping
homologous
superfamilies
 

Description

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
[4, 3]
. These proteins differ widely in size and oligomeric state, and have limited sequence homology
[9]
. 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
[7]
. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices
[2]
, and are mostly dimeric or multimeric, containing at least three conserved regions
[11, 10, 1]
. However, tRNA binding involves an α-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
[6]
.

This entry represents 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) versus AUG (Met) and UGA (stop) versus 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 Escherichia coli and Bacillus subtilis 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
[5]
. 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 α/β domain
[8]
.

References

1.Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Cusack S, Hartlein M, Leberman R. Nucleic Acids Res. 19, 3489-98, (1991). View articlePMID: 1852601

2.Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Perona JJ, Rould MA, Steitz TA. Biochemistry 32, 8758-71, (1993). View articlePMID: 8364025

3.Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. Francklyn C, Perona JJ, Puetz J, Hou YM. RNA 8, 1363-72, (2002). View articlePMID: 12458790

4.Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Woese CR, Olsen GJ, Ibba M, Soll D. Microbiol. Mol. Biol. Rev. 64, 202-36, (2000). View articlePMID: 10704480

5.A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity. Bork P, Koonin EV. Proteins 20, 347-55, (1994). View articlePMID: 7731953

6.Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Wolf YI, Aravind L, Grishin NV, Koonin EV. Genome Res. 9, 689-710, (1999). View articlePMID: 10447505

7.The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. Sugiura I, Nureki O, Ugaji-Yoshikawa Y, Kuwabara S, Shimada A, Tateno M, Lorber B, Giege R, Moras D, Yokoyama S, Konno M. Structure 8, 197-208, (2000). View articlePMID: 10673435

8.Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA. Aravind L, Anantharaman V, Koonin EV. Proteins 48, 1-14, (2002). View articlePMID: 12012333

9.Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Nature 347, 203-6, (1990). View articlePMID: 2203971

10.Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code. Schimmel P. Trends Biochem. Sci. 16, 1-3, (1991). View articlePMID: 2053131

11.The aminoacyl-tRNA synthetase family: modules at work. Delarue M, Moras D. Bioessays 15, 675-87, (1993). View articlePMID: 8274143

GO terms

Cross References

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