Pyridoxal Phosphatase Methods

Evolution

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Structure

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Protein Data Bank (PDB)
The structure of 2cfsA was obtained from the PDB. A search on the database using Pyridoxal Phosphatase's PDB ID (2cfsA) did not yield any results. A search using the PDB ID "2cfs" was successful. The crystal structure of Pyridoxal Phosphatase was obtained from the "Images and Visualization" section located on the right side of website.
http://www.rcsb.org/pdb/explore/explore.do?structureId=2cfs

The PDB file of Pyridoxal Phosphatase was saved for further use.

DALI
DALI, otherwise known as the Distance Alignment Matrix Method, breaks down the input structures into hexapeptide fragments and calculates a distance matrix by evaluating the contact patterns between successive fragments. When two proteins' distance matrices share the same or similar features in approximately the same positions, they can be said to have similar folds with similar-length loops connecting their secondary structure elements.

A search was carried out using the PDB file (obtained from the previous step) of Pyridoxal Phosphatase. The results were generated and returned via e-mail. Due its similarity to 2cfsA, 2oycA - which was at the top of the list of hits generated by the DALI server, was structurally superimposed against 2cfsA using the PyMOL software.

PDBsum
From the EBI website (http://www.ebi.ac.uk/), the PDBsum structural database was accessed to obtain the secondary structures, as well as information (i.e. topology diagram, cleft analysis) pertaining to the secondary structures of both 2cfsA and 2oycA.

Cleft Analysis via PyMOL
Based on the information obtained in the previous step, PyMOL was used to provide a three-dimensional view of potentially active sites in both 2cfsA and 2oycA.

Function

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