Pyridoxal Phosphatase Abstract

Pyridoxal (pyridoxine, vitamin B6) Phosphatase, otherwise known as PLP (or PDXP, in certain cases), is defined as the metabolically active form of the water-soluble Vitamin B6. Its functions involve acting as a cofactor in many reactions of amino acid metabolism, gluconeogenesis and lipid metabolism.

Pyridoxal Phosphatase is an enzyme that catalyses the reaction:

                       Pyridoxal 5'-phosphate + H2O  pyridoxal + phosphate

Based on the provided PDB ID (2cfsA), evolutionary, structural and functional studies were carried out using the provided software with the aim of further characterizing 2cfsA.

A Basic Local Alignment Search Tool (BLAST) search was carried out to determine organisms with similar proteins to 2cfsA. The sequences for selected proteins from the BLAST search was then used to create a multiple sequence alignment where it was found that there were five conserved residues, two residues with conservative substitutions and four that had semi-conservative substitutions. From the multiple sequence alignment, a phylogenetic tree was carried out using Phylip and the data boot-strapped to determine confidence values for the branching. It was found that the closest relatives of 2cfsA (human pyridoxal phosphatase) were rats (Rattus norvegicus), mice ( Mus musculus) and cows (Bos taurus) rather than the ape family, as would have been expected. The 2cfsA protein was connected with proteins in four Kingdoms; Prokaryota, Fungi, Plantae and Animalia, all with differing degrees of relatedness.

In the structural component of this paper, various databases such as DALI and PDBsum were utilized to identify potential structural homology between 2cfsA and the generated protein hits. The practical aspect aside, theoretical research was conducted to provide a clearer insight on the structural properties of both the target and hit proteins. Based on the information provided, several inferences were made regarding the structure of 2cfsA. This information would undoubtedly be important in predicting the functions of the protein-of-interest.

Functional prediction using ProFunc, based on sequence homology and structure, reinforced the function of 2cfsA as a hydrolase. Using STRING, 2cfs_A may be a cofactor to HSPD1 and play a role in protein folding. 2cfs_A had also been predicted to function as a coenzyme for asparagine synthetase using STRING.