Arylformamidase Discussion
probable function
Catalytic triad found in the canonical positions observed in a wide variety of α/β hydrolases.
Functional inference from sequence similarity was restricted due to lack of supporting literature for highest-scoring sequences. Although the function of the arylformamidase from Mus musculus has been relatively well-characterised (Pabarcus 2005), its structure has not been determined. No arylformamidase proteins have not been characterised from amongst the prokaryotes, indicating it may be limited to the eukaryotes. Whilst a high-degree of conservation of the catalytic triad has been observed, there are structurally more similar proteins.
The carboxylesterase 2c7b was chosen for further analysis due to its high structural similarity to 2PBL. 2C7B is a thermostable carboxylesterase from an uncultured archaeon which was isolated in a thermal environmental sample (Byun 2007). This carboxylesterase belongs to a family of bacterial hormone-sensitive lipases/esterases (HSLs) known for their amino-acid sequence similarity to the mammalian hormone-sensitive lipase (Arpigny 1999). Despite the high structural similarity, the catalytic triad as identified in 2CB7 was not conserved in a sequence alignment. This may indicate that sequence alignment is not representative of structural similarities between 2CB7 and 2PBL.
There were a number of other bacterial HSL proteins as identified by Byun, et al. (2007) found to have a high structural similarity to 2PBL. Although a relatively low sequence similarity with 2PBL was observed, regions of conserved sequence characteristic to HSL proteins (Arpigny 1999) aligned with 2PBL. This may indicate that 2PBL is a member of the bacterial HSL family of lipolytic proteins. However, conservation of the catalytic triad is still poor.
The HSL family encompasses a broad range of proteins with diverse functionality. Even though a number of HSL proteins have been determined and were included in the structure search, 2c7b was still returned as the most similar structure, indicating that 2pbl may in fact be a carboxylesterase. Specifically, carboxylesterases are involved in a broad range of reactions. Fundamentally, they catalyze the hydration of carboxyl esters into an alcohol and a carboxylic acid (see …).
Further analysis revealed that 2pbl shared greater structural similarity with thermostable esterases of the HSL family compared to its other members. As discussed, thermostable proteins such as 2c7b often exist in dimers, a possiblity which remains uninvestigated for 2pbl.
Phylogeny
The multiple sequence alignment revealed several conserved regions accross all species, thereby indicating a high level of conservation from Bacteria through Eukaryota. Most significantly, the catalytic triad of 137S, 215E/D and 242H and many associated residues which occur in the same structural area of the protein are conserved accross all species of prokaryotes and eukaryotes. This may therefore be indicative of the conservation of functional group of residues within the protein. These included vertebrates, invertebrates, yeasts, moulds and single-celled eukaryotes. The catalytic triad is thought to be involved in thioesterase/carboxylesterase activity though the function of the protein may show variation between species.
Given that the phylogeny of our protein is largely consistent with traditional taxonomic groupings of organisms and that we can find no evidence of horizontal gene transfer, the delineations between prokariotic and eukaryotic species allow us to infer that the dominant mode of inheritance is clonal from bacteria to plantae and animalia.
biological implications/applications...
Potential thermostability - applicability in industry.
further research...
