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. Diagram and caption courtesy of Almo et al., 2007.]][[Image: | [[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. Diagram and caption courtesy of Almo et al., 2007.]][[Image:2CFS_MG_Active_Site2.JPG|left|thumb|400px|Fig 13. 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 Figs 10 and 11.]] | ||
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Revision as of 02:00, 9 June 2008
Importance of structural studies - the relationship between Evolution, Structure and Function.
- Protein 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.
![](/mediawiki/upload/thumb/7/78/2cftA_Structure_breakdown.jpg/500px-2cftA_Structure_breakdown.jpg)
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...
Comparing 2oycA against 2cfsA
1. Secondary Structure
2. Topology Diagram
PROFUNC
Related Protein Sequences in the PDB (SAS)
Matches to existing PDB Structures
Secondary Structure Matching (SSM)
![](/mediawiki/upload/thumb/0/0a/LIGPLOT_2cftA.jpg/400px-LIGPLOT_2cftA.jpg)
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.