Aminoacyl-tRNA synthetases (EC 6.1.1.-)  are a group of enzymes which
activate amino acids and transfer them to specific tRNA molecules as the first
step in protein biosynthesis. In prokaryotic organisms there are at least
twenty different types of aminoacyl-tRNA synthetases, one for each different
amino acid. In eukaryotes there are generally two aminoacyl-tRNA synthetases
for each different amino acid: one cytosolic form and a mitochondrial form.
While all these enzymes have a common function, they are widely diverse in
terms of subunit size and of quaternary structure.
The synthetases specific for alanine, asparagine, aspartic acid, glycine,
histidine, lysine, phenylalanine, proline, serine, and threonine are referred
to as class-II synthetases [2,3,4,5,6]. Class-II enzymes are generally dimeric or
tetrameric, and attach their amino acid to the 3' OH of their tRNA, except for
phenylalaninyl-tRNA synthetase which uses the 2' OH like the class-I tRNA
Class-II tRNA synthetases are structurally distinct from the class-I enzymes
and have a central antiparallel β-sheet instead of the Rossman fold found
in Class-I structure (see <PDB:1SES>) .
Class-II tRNA synthetases do not share a high degree of similarity, however at
least three conserved regions are present [2,5,9]. We have developed three
profiles to detect class-II tRNA synthetases. The first one recognize all
class-II enzymes except for heterodimeric glycyl-tRNA synthetases and alanyl-tRNA synthetases which are picked up by specific profiles.
There are at least two families of proteins related to class-II enzymes and
that are also recognized by the first profile.
- Bacterial aspartate--ammonia ligase (EC 184.108.40.206), the enzyme that produces
asparagine from aspartate .
- Bacterial ATP phosphoribosyltransferase regulatory subunit (gene hisZ).
HisZ seems to allow the regulation of ATP phosphoribosyltransferase
activity by histidine. It is distantly related to histidyl-tRNA synthetases
and not all members of this family are picked up by the profile.
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