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Appropriate attachment of an amino acid to its cognate tRNA is the key to
faithful translation of the genetic code. The family of enzymes responsible
for this is the aminoacyl-tRNA synthetases (AATRSs) (EC 6.1.1.-).
AATRSs catalyse a two-step reaction:
(1) Enzyme + amino acid + ATP ---> Enzyme(aminoacyl-AMP) + PPi
(2) tRNA + Enzyme(aminoacyl-AMP) ---> aminoacyl-tRNA + AMP + Enzyme
In the first step, they form an aminoacyl-adenylate, in which the carboxyl
of the amino acid is linked to the alpha-phosphate of ATP, by displacing
the pyrophosphate. When the correct tRNA is bound, the aminoacyl group is
transferred to the 2'- or 3'-terminal OH of the tRNA at the expense of AMP
Based on structural and sequence comparisons, this group of at least 20
proteins (in prokaryotes there are approximately 20, but in eukaryotes
there are usually 2 forms for each amino acid; namely, the cytosolic and
mitochondrial forms) can be divided into two classes.
Class I AATRSs contain a characteristic Rossman fold and are mostly
monomeric. At the primary structure level, two highly-conserved motifs
are observed, `HIGH' and `KMSKS' [2,3]; these are associated with the ATP-
Class II AATRSs share an anti-parallel beta-sheet formation, flanked by
alpha-helices , and are mostly dimeric or multimeric.
Further distinction between the two classes is evident when the reaction
mechanisms are investigated. In reactions catalysed by the class I AATRSs,
the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in
class II reactions, the 3'-hydroxyl site is preferred.
Glycyl-tRNA synthetase (EC 184.108.40.206) is specific to glycine and belongs to
class II. It is one of the most complex synthetases, existing as either an
alpha(2) dimer or alpha(2)-beta(2) tetramer [4-6]. 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 and beta subunits also lack significant sequence similarity.
However, they are translated from a single mRNA , and a single chain
glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have
significant similarity with both domains, suggesting divergence from a
single polypeptide chain .
TRNASYNTHGA is a 6-element fingerprint that provides a signature for the
glycyl-tRNA synthetase alpha subunit. The fingerprint was derived from an
initial alignment of 5 sequences: the motifs were drawn from conserved
regions spanning the full alignment length - motif 5 includes the region
encoded by PROSITE pattern AA_TRNA_LIGASE_II_2 (PS00339). Two iterations
on OWL30.2 were required to reach convergence, at which point a true set
comprising 11 sequences was identified. A single partial match was found,
PFY145682, a fragment that lacks the portion of sequence bearing motif 6.
An update on SPTR37_9f identified a true set of 11 sequences.