Pyridoxal Phosphatase structure: Difference between revisions
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[[Image:Cleft Analysis PyMOL 2cfsA V2.jpg|left|thumb|300px|Back View of 2cfsA & its potential binding sites, as generated using PyMOL]][[Image:Cleft Analysis PyMOL 2oycA V2.jpg|left|thumb|300px|Back View of 2oycA & its potential binding sites, as generated using PyMOL]] | [[Image:Cleft Analysis PyMOL 2cfsA V2.jpg|left|thumb|300px|Back View of 2cfsA & its potential binding sites, as generated using PyMOL]][[Image:Cleft Analysis PyMOL 2oycA V2.jpg|left|thumb|300px|Back View of 2oycA & its potential binding sites, as generated using PyMOL]] | ||
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Based on other information obtained from the database, 2cfsA was identified to belong to the Haloacid Dehalogenase (HAD) superfamily. Members of this protein family catalyze phosphoryl transfer of small molecules by co-ordinating the magnesium ions. The substitution of magnesium ions with calcium ions results in a near complete loss of activity. The conclusion, therefore, is that the catalytic site has to be in the region consisting of the magnesium ions. | |||
Revision as of 01:20, 10 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 - Similarities
1. Secondary Structure
2. Topology Diagram
3. Cleft Analysis (PyMOL)
Based on other information obtained from the database, 2cfsA was identified to belong to the Haloacid Dehalogenase (HAD) superfamily. Members of this protein family catalyze phosphoryl transfer of small molecules by co-ordinating the magnesium ions. The substitution of magnesium ions with calcium ions results in a near complete loss of activity. The conclusion, therefore, is that the catalytic site has to be in the region consisting of the magnesium ions.
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 one of 2cfsA's magnesium ions (Mg1296). What is the significance? Substitution of the magnesium ion with the catalytically inert calcium ion results in a near-complete loss of activity.
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.