Pyridoxal Phosphatase structure: Difference between revisions
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[[Image:Catalytic_Site_of_2cftA.jpg|left|thumb|400px|The catalytic site of 2cftA, with its PLP ligand and inhibitory calcium ion. As illustrated, the calcium ion is hepta-coordinated and participates in a bidentate interaction with the active site nucleophile Asp-25, resulting in a loss of activity. Diagram and caption courtesy of Almo et al., 2007.]][[Image:2CFS_MG_Active_Site2.JPG|left|thumb|400px|The three-dimensional visualization of the catalytic site of 2cfsA. This was generated based on the location of the residues constituting the catalytic site, as provided in the LIGPLOT diagrams pertaining to the interactions involving 2cfsA's magnesium ions]] | [[Image:Catalytic_Site_of_2cftA.jpg|left|thumb|400px|The catalytic site of 2cftA, with its PLP ligand and inhibitory calcium ion. As illustrated, the calcium ion is hepta-coordinated and participates in a bidentate interaction with the active site nucleophile Asp-25, resulting in a loss of activity. Diagram and caption courtesy of Almo et al., 2007.]][[Image:2CFS_MG_Active_Site2.JPG|left|thumb|400px|The three-dimensional visualization of the catalytic site of 2cfsA. This was generated based on the location of the residues constituting the catalytic site, as provided in the LIGPLOT diagrams pertaining to the interactions involving 2cfsA's magnesium ions]] | ||
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Based on the above images, the calcium ion (2cftA) is at the same location as 2cfsA's magnesium ion (Mg | |||
'''Dali - 2nd Run''' <BR> | '''Dali - 2nd Run''' <BR> |
Revision as of 12:55, 9 June 2008
Importance of structural studies - the relationship between Evolution, Structure and Function.
- Evolution provides information pertaining to families of structurally related proteins, BUT sequence identities may be low.
- Structural studies help to identify unanticipated relationships in known structures.
- Functions can be assigned based on structural studies.
(Some of the) Results obtained during this study

DALI - 1st Run
Based on the results of the first run, how similar is 2oycA to 2cfsA? With the aid of PyMOL, 2oycA was super-imposed against 2cfsA...
2cfsA vs 2oycA
1. Secondary Structure
2. Topology Diagram
2. Cleft Analysis (PyMOL)
PROFUNC
Related Protein Sequences in the PDB (SAS)
Matches to existing PDB Structures
Secondary Structure Matching (SSM)

Based on the above images, the calcium ion (2cftA) is at the same location as 2cfsA's magnesium ion (Mg
Dali - 2nd Run
"Inconsistencies" - flaw or strength?
The second DALI run does not affect the results as PROFUNC has already indicated 2cftA to be the most closely-related to 2cfsA. On the contrary, the results serve as a confirmation that 2cfsA is indeed a Pyridoxal Phosphatase and belongs to the same family as 2oycA and 2cftA - two proteins that have been studied to assist in the structural and functional prediction of 2cfsA.