Pyridoxal Phosphatase Results: Difference between revisions
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==Evolution== | |||
===Multiple Sequence Alignment=== | |||
[[Image:Pyridoxal_phosphatase_MSA_sequences_conserved .jpg]] | [[Image:Pyridoxal_phosphatase_MSA_sequences_conserved .jpg]] | ||
==Structure== | |||
<br> | |||
===General Structure of Pyridoxal Phosphatase=== | |||
[[Image:2cftA Structure breakdown.jpg|left|thumb|500px|Fig 1. Courtesy (and edited) of Almo et al., 2007. This structure is actually that of 2cftA - Human Pyridoxal 5'-Phosphate Phosphatase with its substrate. It is similar to 2cfsA, with the differences being the presence of a PLP ligand and the type of metal ions (2cfsA has magnesium ions, 2cftA has calcium ions). Notice the similarities between the structure of 2cftA and 2cfsA (Fig 2.).]] | [[Image:2cftA Structure breakdown.jpg|left|thumb|500px|Fig 1. Courtesy (and edited) of Almo et al., 2007. This structure is actually that of 2cftA - Human Pyridoxal 5'-Phosphate Phosphatase with its substrate. It is similar to 2cfsA, with the differences being the presence of a PLP ligand and the type of metal ions (2cfsA has magnesium ions, 2cftA has calcium ions). Notice the similarities between the structure of 2cftA and 2cfsA (Fig 2.).]] | ||
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===PDB===<BR> | |||
Based on the information provided in the website, Pyridoxal Phosphatase has the following characteristics: | Based on the information provided in the website, Pyridoxal Phosphatase has the following characteristics: | ||
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http://www.rcsb.org/pdb/explore/explore.do?structureId=2cfs<BR> | http://www.rcsb.org/pdb/explore/explore.do?structureId=2cfs<BR> | ||
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===DALI===<BR> | |||
[[Image:Dali cutoff.jpg|right|thumb|550px|Fig 3. Significant hits as generated from the DALI database]] | [[Image:Dali cutoff.jpg|right|thumb|550px|Fig 3. Significant hits as generated from the DALI database]] | ||
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===PDBsum=== <BR> | |||
[[Image:2cfsA Coloured.jpg|right|thumb|400px|Fig 5. Three different views of 2cfsA, courtesy of PDBsum]] | [[Image:2cfsA Coloured.jpg|right|thumb|400px|Fig 5. Three different views of 2cfsA, courtesy of PDBsum]] | ||
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===PROFUNC=== <BR> | |||
''Related Protein Sequences in the PDB (SAS)''<BR> | ''Related Protein Sequences in the PDB (SAS)''<BR> | ||
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Based on the above-mentioned results, it was concluded that 2cfsA, 2cftA and 2oycA were structurally similar, and that further functional studies could indeed uncover the function of the protein-of-interest: 2cfsA <BR> | Based on the above-mentioned results, it was concluded that 2cfsA, 2cftA and 2oycA were structurally similar, and that further functional studies could indeed uncover the function of the protein-of-interest: 2cfsA <BR> | ||
==Function== | |||
Revision as of 07:58, 3 June 2008
Evolution
Multiple Sequence Alignment
Structure
General Structure of Pyridoxal Phosphatase

===PDB===
Based on the information provided in the website, Pyridoxal Phosphatase has the following characteristics:
- Pyridoxal Phosphatase is isolated from Homo Sapiens and is expressed in Escherichia Coli.
- Structure is similar to the Pyridoxal Phosphate Phospatase protein
- 1 (A) Chain
- Consists of Magnesium components
- Resolution of 2.40 angstroms. This means that the number of sidechains in the wrong rotamer is smaller as compared to proteins of a higher resolution (>2.5 angstroms). Other characteristics of proteins of similar resolutions are: (1) many small detectable errors, (2) correct folding, (3) fewer number of errors in the surface loops and (4) visible water molecules and small ligands.
http://www.rcsb.org/pdb/explore/explore.do?structureId=2cfs
===DALI===
A total of 176 hits were generated, of which only the first 11 (as shown in Fig. 3) were predicted to be significant. The others were rejected on account that their respective nres scores (refer to the red, boxed section) were less than half of Pyridoxal Phosphatase's (nres: 296).
It was noted that none of the hits actually matched 2cfsA. The closest was a Pyridoxal Phosphate Phosphatase (PDB ID 2oycA) which based on the results, was predicted to be highly similar to 2cfsA. Table 1 highlights the similarities between Pyridoxal Phosphatase (2cfsA) and the Pyridoxal Phosphate Phosphatase (2oycA)
Using the PyMOL software, 2oycA was superimposed against 2cfsA, and both structures, as shown in Fig. 4, are structurally similar.
===PDBsum===
Fig. 5 offers three different views of 2cfsA. The purple chains represent the amino acid chain of 293 amino acids while the green spheres represent the magnesium ions (x2).
By clicking the "Protein chain" link, the user was re-directed to a website containing information pertaining to the secondary structures of both 2cfsA and 2oycA.
Secondary Structures of 2cfsA (L, http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl) and 2oycA (R)
Topology diagrams of 2cfsA (Fig 6.1. http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2cfs&template=protein.html&r=wiring&l=1&chain=A) and 2oycA (Fig 6.2).
Cleft Analyses of 2cfsA (Fig 7.1. http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2cfs&template=clefts.html&pdbcode=2cfs&r=speedfill) and 2oycA (Fig 7.2).
Cleft Analysis via PyMol
===PROFUNC===
Related Protein Sequences in the PDB (SAS)
Matches to existing PDB Structures
Secondary Structure Matching (SSM)
PyMOL generation of potential active site
A search on 2oycA was also carried out via PROFUNC, and consistency in the results confirmed that 2cfsA and 2oycA were indeed structurally similar. This lends weight to the original hypothesis that they could be functionally related. In fact, based on the Nest Analysis method, 2oycA was observed to be sharing a large number of active sites. The results of the Nest Analysis (2oycA) are as shown below. Notice the similarities between the active sites of both 2oycA and 2cfsA.
In addition, the predicted function of 2oycA was similar to 2cfsA.

Based on the above-mentioned results, it was concluded that 2cfsA, 2cftA and 2oycA were structurally similar, and that further functional studies could indeed uncover the function of the protein-of-interest: 2cfsA