Pyridoxal Phosphatase Discussion
Evolution
Structure
PDB
Based on the information obtained from PDB, 2cfsA was identified to have the following features:
- Isolated from Homo Sapiens, and is expressed in Escherichia Coli.
- Structurally similar to the Pyridoxal Phosphate Phosphatase protein.
- Consists of a single type of chain (A), and (2) Magnesium components.
- Resolution of 2.4 angstroms. The significance of this is that the probability that the number of side-chains in the wrong rotamer is relatively smaller. Proteins of similar resolution were noted also to: (1) have many small detectable errors, (2) be of correct folding, (3) contain fewer number of errors in the surface loops and (4) consist of visible water molecules and small ligands.
DALI
A search on the protein in the Dali database yielded 176 hits, of which the top 11 were identified to be of potential significance on account of the information provided in the summary block of the results. The summary block provides the following information:
- Z score, or the statistical significance of the similarity between the hit protein and the protein-of-interest.
- Root Mean Square Distance (RMSD), which indicates the degree of divergence between the hit protein and the protein-of-interest.
- lali, the total number of shared residues between the hit protein and the protein-of-interest.
- nres, or the total number of residues in the hit protein.
- %id. As the term implies, %id refers to the percentage of sequence identity over structurally identical positions.
Of the 11 hit proteins, 2oycA was predicted to be the most structurally similar to 2cfsA. This was on virtue of the following properties:
- Among the list of hit proteins generated, it had the highest Z value of 47.6
- rmsd value of 0.4, the lowest among the hit proteins. The lower the rmsd value, the more similar it is to the protein-of-interest.
- lali value of 288. 2cfsA has a total of 298 amino acid residues, which means that 2oycA and 2cfsA differ by only 10 amino acid residues.
- nres value of 292. This did not bear much significance on the decision-making process. However, a conclusion drawn was that it was similar to 2cfsA in terms of length.
- %id score of 99%, which simply means that based on the information currently stored in the DALI database, 2oycA and 2cfsA were highly similar.
To further prove that 2cfsA and 2oycA were structurally similar, their three dimensional structures were superimposed using PyMOL. As expected, the 2oycA bore a close resemblance to 2cfsA, but the differing regions have yet to be identified.
Function
