Alanyl-tRNA Synthetase

Alanyl-tRNA synthetase (AlaRS) is an enzyme that plays a crucial role in protein synthesis by catalyzing the attachment of the amino acid alanine to its cognate tRNA: $ \text{Ala} + \text{tRNA}^\text{Ala} + \text{ATP} \xrightarrow{\text{AlaRS}} \text{Ala-tRNA}^\text{Ala} + \text{AMP} + \text{PP}_i $ The catalytic core of AlaRS is similar to the bacterial-like [GlyRS-B](/class2/gly2), which together comprise subclass IId (Valencia-Sánchez et al. 2016). The alpha helix rich tRNA binding domain primarily recognises elements within the tRNA acceptor stem (Naganuma et al. 2009). Although the catalytic domain of AlaRS is one of the smallest in the superfamily, the full enzyme is quite large and contains a unique domain architecture. Homodimerization in AlaRS occurs via a C-terminal coiled coil, unlike most class II synthetases which dimerise at the catalytic core (Naganuma et al. 2009). However, in certain organisms such as *Nanoarchaeum equitans*, AlaRS is produced by two genes which express the N- and C-terminal regions respectively, and thus likely behaves as a heterotetramer in such systems (Arutaki et al. 2020). The fusion or fission of AARS genes that result in switching between homodimeric and heterotetrameric enzymes has also been observed in GlyRS-B and [PylRS](/class2/pyl). The catalytic domains of AlaRS and GlyRS-B are characterized by their absence of the small interface between motifs 1 and 2 (Douglas et al. 2023). The small interface promotes dimerisation in other Class II synthetases, and therefore AlaRS and GlyRS-B form oligomers through alternative means. However, like most Class II synthetases, ATP binding is coordinated by the arginine tweezers, located in motifs 2 and 3 (Kaiser et al. 2018). In bacteria and eukaryotes, the AlaRS catalytic domain is characterized by the 30-40 residue AlaRS insertion module between motifs 2 and 3. The module is stabilized by a short $\beta$ strand that runs parallel with the six stranded antiparallel fold of the catalytic domain. This module is absent in archaea. Editing in AlaRS occurs at the post-transfer level through an editing domain which expunges mischarged glycyl and seryl groups from tRNA$^\text{Ala}$ (Tsui et al. 1981, Guo et al. 2009b). AlaX proteins, which are homologous with the editing domain, also target Ser-tRNA$^\text{Ala}$ (Beebe et al. 2008). This double checkpoint system minimizes serine-for-alanine mistranslations, which are known to cause profound problems in nature (Guo et al. 2009a, Schimmel 2011). The C-ala domain is tethered to the editing domain through a coiled coil and promotes cooperative binding between the catalytic core and the editing domains to tRNA$^\text{Ala}$ (Guo et al. 2009b). The [editing domain](/superfamily/class2/Editing_domain_AT/) of AlaRS is downstream of the catalytic domain and is homologous with that of [ThrRS](/class2/thr/), which conversely resides upstream of the catalytic domain (Sankaranarayanan et al. 1999). In eukaryotes, AlaRS is one of the few aminoacyl-tRNA synthetases which operate in both the cytoplasm and mitochondria, alongside [GlyRS](/class2/gly3), [HisRS](/class2/his/), and [ValRS](/class1/val/). The two forms of AlaRS were likely of organellar, and hence bacterial, origin. Therefore, the archaeal form of AlaRS stands apart from the rest of the family. Localisation into these compartments is achieved through alternative initiation, which governs the expression of an N-terminal mitochondrial localisation signal (Tang et al. 2004). One exception to this is the AlaRS of the yeast *Vanderwaltozyma polyspora*, which has two genes encoding AlaRS; one for either compartment (Chang et al. 2011). It is likely that these two genes arose from a recent duplication event.

References

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