http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&feed=atom&action=historyPyridoxal Phosphatase Discussion - Revision history2024-03-29T15:41:55ZRevision history for this page on the wikiMediaWiki 1.39.6http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10697&oldid=prevSitoh Kheng Wai: /* PDBsum */2008-06-10T01:23:27Z<p><span dir="auto"><span class="autocomment">PDBsum</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 01:23, 10 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l72">Line 72:</td>
<td colspan="2" class="diff-lineno">Line 72:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Other structural studies indicated the use of the Combinatorial Extension (CE) database. In this study, the CE database was not utilized due to software incompatibility. Whenever a query PDB ID was run against the database, an error message would appear. This could be because CE only accepts structures uploaded from a Mac or a Unix workstation (Novotny et al., 2004), which were not utilized during this study.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Other structural studies indicated the use of the Combinatorial Extension (CE) database. In this study, the CE database was not utilized due to software incompatibility. Whenever a query PDB ID was run against the database, an error message would appear. This could be because CE only accepts structures uploaded from a Mac or a Unix workstation (Novotny et al., 2004), which were not utilized during this study.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>===PDBsum===</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>===PDBsum<ins style="font-weight: bold; text-decoration: none;">, Pfam</ins>===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>PDBsum is a database which pictorially illustrates information on each macromolecule deposited in the PDB. Some of the features provided by PDBsum include:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>PDBsum is a database which pictorially illustrates information on each macromolecule deposited in the PDB. Some of the features provided by PDBsum include:</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Images of the query structure</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Images of the query structure</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l90">Line 90:</td>
<td colspan="2" class="diff-lineno">Line 90:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The results obtained are significant as structural information is usually crucial for the functional prediction of the protein-of-interest. Since the information provided by the secondary structures of both proteins are highly similar, there is a great possibility that 2cfsA and 2oycA are functionally similar. <BR></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The results obtained are significant as structural information is usually crucial for the functional prediction of the protein-of-interest. Since the information provided by the secondary structures of both proteins are highly similar, there is a great possibility that 2cfsA and 2oycA are functionally similar. <BR></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2cfsA <del style="font-weight: bold; text-decoration: none;">was </del>identified <del style="font-weight: bold; text-decoration: none;">to be from </del>the haloacid dehalogenase-like hydrolase family (http://pfam.sanger.ac.uk/family?acc=PF00702). Members of this protein family (which includes phosphatases) belong to the Haloacid Dehalogenase (HAD) superfamily. Almo et al., 2007 mentions that members of the HAD superfamily catalyze phosphoryl transfer reactions in small molecules. It encompasses a large number of magnesium-dependent phosphohydrolases which are responsible for the co-ordination of the catalytically active magnesium ions, where the first aspartic acid serves as the nucleophile and phosphoryl acceptor. Further evidence highlighting the importance of the magnesium ions lie in the fact that when substituted with calcium, a near total loss of activity is observed. This highlights the significance of the magnesium ion, and also ties in with the work done using the ProFunc database, which predicts that 2cfsA is involved in catalytic processes. An assumption, therefore, would be that the magnesium ions are involved in the catalytic functions of 2cfsA.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">A link to the pfam site pertaining to </ins>2cfsA identified <ins style="font-weight: bold; text-decoration: none;">it as a member of </ins>the haloacid dehalogenase-like hydrolase family (http://pfam.sanger.ac.uk/family?acc=PF00702). Members of this protein family (which includes phosphatases) belong to the Haloacid Dehalogenase (HAD) superfamily. Almo et al., 2007 mentions that members of the HAD superfamily catalyze phosphoryl transfer reactions in small molecules. It encompasses a large number of magnesium-dependent phosphohydrolases which are responsible for the co-ordination of the catalytically active magnesium ions, where the first aspartic acid serves as the nucleophile and phosphoryl acceptor. Further evidence highlighting the importance of the magnesium ions lie in the fact that when substituted with calcium, a near total loss of activity is observed. This highlights the significance of the magnesium ion, and also ties in with the work done using the ProFunc database, which predicts that 2cfsA is involved in catalytic processes. An assumption, therefore, would be that the magnesium ions are involved in the catalytic functions of 2cfsA.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===PROFUNC===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===PROFUNC===</div></td></tr>
</table>Sitoh Kheng Waihttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10355&oldid=prevDuguoqing: /* Function */2008-06-09T21:10:28Z<p><span dir="auto"><span class="autocomment">Function</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:10, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l113">Line 113:</td>
<td colspan="2" class="diff-lineno">Line 113:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>None of the search results indicates that 2cfs_A have other functions. Likewise for structure comparision, using Interpro and Profunc, top search results yield only members of the HAD-like hydrolase superfamily. The use of sequence homology and structure similarities in this case to predict functions seemed inefficient as search results based on sequence and structure are only able to pinpoint that 2cfs_A functions as a HAD-like hydrolase and are unable to give more information beyond that.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>None of the search results indicates that 2cfs_A have other functions. Likewise for structure comparision, using Interpro and Profunc, top search results yield only members of the HAD-like hydrolase superfamily. The use of sequence homology and structure similarities in this case to predict functions seemed inefficient as search results based on sequence and structure are only able to pinpoint that 2cfs_A functions as a HAD-like hydrolase and are unable to give more information beyond that.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>===<del style="font-weight: bold; text-decoration: none;">Protein</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>===<ins style="font-weight: bold; text-decoration: none;">Functional Expression in Tissue===</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Function of Pyridoxal Phosphatase has been well established as it is a very important vitamin, involved in most cellular metabolism and reactions. However, the level of functional expression is markedly variable from tissue to tissue. In adults, PLP phosphatase was most highly expressed in all the regions of central nerve system except the spinal cord. High levels were also found in liver and testis. In fetus, expression levels of PLP phosphatase transcript showed a rather even distribution in all organs except the brain.It is interesting to note, levels of pyridoxal phosphatase in the brain for both adults and fetus are substantially higher, suggesting that pyridoxal phosphatase may have a specific functional role there.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>===<del style="font-weight: bold; text-decoration: none;">Functional Expression in Tissue</del>===</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>===<ins style="font-weight: bold; text-decoration: none;">Protein-Protein Interaction</ins>===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Function </del>of <del style="font-weight: bold; text-decoration: none;">Pyridoxal Phosphatase has been well established as it is a very important vitamin</del>, <del style="font-weight: bold; text-decoration: none;">involved in most cellular metabolism and reactions. However</del>, <del style="font-weight: bold; text-decoration: none;">the level of functional expression of pyridoxal phosphatase differs from tissue to tissue</del>. <del style="font-weight: bold; text-decoration: none;">It </del>is <del style="font-weight: bold; text-decoration: none;">interesting </del>to <del style="font-weight: bold; text-decoration: none;">note, levels of pyridoxal phosphatase in </del>the <del style="font-weight: bold; text-decoration: none;">brain is substantially higher, suggesting that pyridoxal phosphatase may have a specific functional role there</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Using STRING, predicted functional partners for protein of interest can be predicted, based on proximity </ins>of <ins style="font-weight: bold; text-decoration: none;">gene location</ins>, <ins style="font-weight: bold; text-decoration: none;">interaction discovered during experiments</ins>, <ins style="font-weight: bold; text-decoration: none;">textmining etc</ins>. <ins style="font-weight: bold; text-decoration: none;">This </ins>is <ins style="font-weight: bold; text-decoration: none;">very useful as there are evidence </ins>to <ins style="font-weight: bold; text-decoration: none;">form the basis for </ins>the <ins style="font-weight: bold; text-decoration: none;">prediction</ins>. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=====back to [[Pyridoxal Phosphatase]] main page=====</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=====back to [[Pyridoxal Phosphatase]] main page=====</div></td></tr>
</table>Duguoqinghttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10354&oldid=prevDuguoqing: /* Function */2008-06-09T20:54:35Z<p><span dir="auto"><span class="autocomment">Function</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:54, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l108">Line 108:</td>
<td colspan="2" class="diff-lineno">Line 108:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">===Sequence and Structure===</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Search results from Pfam, FASTA and BLAST database all pinpoints that 2cfs_A belongs to HAD-like hydrolase superfamily.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">None of the search results indicates that 2cfs_A have other functions. Likewise for structure comparision, using Interpro and Profunc, top search results yield only members of the HAD-like hydrolase superfamily. The use of sequence homology and structure similarities in this case to predict functions seemed inefficient as search results based on sequence and structure are only able to pinpoint that 2cfs_A functions as a HAD-like hydrolase and are unable to give more information beyond that.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">===Protein</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">===Functional Expression in Tissue===</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Function of Pyridoxal Phosphatase has been well established as it is a very important vitamin, involved in most cellular metabolism and reactions. However, the level of functional expression of pyridoxal phosphatase differs from tissue to tissue. It is interesting to note, levels of pyridoxal phosphatase in the brain is substantially higher, suggesting that pyridoxal phosphatase may have a specific functional role there.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Function of Pyridoxal Phosphatase has been well established as it is a very important vitamin, involved in most cellular metabolism and reactions. However, the level of functional expression of pyridoxal phosphatase differs from tissue to tissue. It is interesting to note, levels of pyridoxal phosphatase in the brain is substantially higher, suggesting that pyridoxal phosphatase may have a specific functional role there.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=====back to [[Pyridoxal Phosphatase]] main page=====</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=====back to [[Pyridoxal Phosphatase]] main page=====</div></td></tr>
</table>Duguoqinghttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10353&oldid=prevDuguoqing: /* Function */2008-06-09T20:38:05Z<p><span dir="auto"><span class="autocomment">Function</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:38, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l108">Line 108:</td>
<td colspan="2" class="diff-lineno">Line 108:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Function of Pyridoxal Phosphatase has been well established as it is a very important vitamin, involved in most cellular metabolism and reactions. However, the level of functional expression of pyridoxal phosphatase differs from tissue to tissue. It is interesting to note, levels of pyridoxal phosphatase in the brain is substantially higher, suggesting that pyridoxal phosphatase may have a specific functional role there.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=====back to [[Pyridoxal Phosphatase]] main page=====</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=====back to [[Pyridoxal Phosphatase]] main page=====</div></td></tr>
</table>Duguoqinghttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10313&oldid=prevSitoh Kheng Wai: /* PROFUNC */2008-06-09T17:04:44Z<p><span dir="auto"><span class="autocomment">PROFUNC</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:04, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l101">Line 101:</td>
<td colspan="2" class="diff-lineno">Line 101:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In terms of secondary structure matching (SSM), however, 2cftA was NOT identical to 2cfsA, as reflected by their differing Q scores (1.000 and 0.981 respectively). The Q score takes into account the number of aligned residues, the rmsd scores and the size of the proteins; and a high Q score implies high similarity between the hit protein and the protein-of-interest. More interestingly, however, was the observation that 2oycA was a distant sixth on the list, four tiers below 2cftA. Such was the homology between the hit proteins and 2cfsA, however, that even at sixth, the deviation between 2cfsA and 2oycA was minimal. <BR></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In terms of secondary structure matching (SSM), however, 2cftA was NOT identical to 2cfsA, as reflected by their differing Q scores (1.000 and 0.981 respectively). The Q score takes into account the number of aligned residues, the rmsd scores and the size of the proteins; and a high Q score implies high similarity between the hit protein and the protein-of-interest. More interestingly, however, was the observation that 2oycA was a distant sixth on the list, four tiers below 2cftA. Such was the homology between the hit proteins and 2cfsA, however, that even at sixth, the deviation between 2cfsA and 2oycA was minimal. <BR></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>To determine the potential active sites of 2cfsA, the nest analysis method was utilized. Based on an article by Pal et. al, 2002, the principle of this method revolves around the possibility that anion (negatively-charged) and cation (positively-charged) binding sites in proteins are made up of three amino acids, of which two exhibit "enantiomeric" main chain conformations. This simply means that the main chain torsion angles of the two adjacent amino acids are inverted about the centre of the Ramachandran plot. This results in the formation of "nests", which are defined as concave depressions which ultimately serve as binding sites. Using the nest analysis method, 2oycA obtained similar results to that of 2cfsA. Keeping in mind that 2oycA is the PDB identifier for Chronophin, and that there is an article covering chronophin, it was used to identify potential structure-function relationships.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>To determine the potential active sites of 2cfsA, the nest analysis method was utilized. Based on an article by Pal et. al, 2002, the principle of this method revolves around the possibility that anion (negatively-charged) and cation (positively-charged) binding sites in proteins are made up of three amino acids, of which two exhibit "enantiomeric" main chain conformations. This simply means that the main chain torsion angles of the two adjacent amino acids are inverted about the centre of the Ramachandran plot. This results in the formation of "nests", which are defined as concave depressions which ultimately serve as binding sites. Using the nest analysis method, 2oycA obtained similar results to that of 2cfsA<ins style="font-weight: bold; text-decoration: none;">. There is therefore a good chance that both 2cfsA and 2oycA have similar catalytic sites</ins>. Keeping in mind that 2oycA is the PDB identifier for Chronophin, and that there is an article covering chronophin, it was used to identify potential structure-function relationships.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Visualizing the potential catalytic site of 2cfsA===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Visualizing the potential catalytic site of 2cfsA===</div></td></tr>
</table>Sitoh Kheng Waihttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10309&oldid=prevSitoh Kheng Wai: /* PROFUNC */2008-06-09T17:03:27Z<p><span dir="auto"><span class="autocomment">PROFUNC</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:03, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l101">Line 101:</td>
<td colspan="2" class="diff-lineno">Line 101:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In terms of secondary structure matching (SSM), however, 2cftA was NOT identical to 2cfsA, as reflected by their differing Q scores (1.000 and 0.981 respectively). The Q score takes into account the number of aligned residues, the rmsd scores and the size of the proteins; and a high Q score implies high similarity between the hit protein and the protein-of-interest. More interestingly, however, was the observation that 2oycA was a distant sixth on the list, four tiers below 2cftA. Such was the homology between the hit proteins and 2cfsA, however, that even at sixth, the deviation between 2cfsA and 2oycA was minimal. <BR></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In terms of secondary structure matching (SSM), however, 2cftA was NOT identical to 2cfsA, as reflected by their differing Q scores (1.000 and 0.981 respectively). The Q score takes into account the number of aligned residues, the rmsd scores and the size of the proteins; and a high Q score implies high similarity between the hit protein and the protein-of-interest. More interestingly, however, was the observation that 2oycA was a distant sixth on the list, four tiers below 2cftA. Such was the homology between the hit proteins and 2cfsA, however, that even at sixth, the deviation between 2cfsA and 2oycA was minimal. <BR></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>To determine the potential active sites of 2cfsA, the nest analysis method was utilized. Based on an article by Pal et. al, 2002, the principle of this method revolves around the possibility that anion (negatively-charged) and cation (positively-charged) binding sites in proteins are made up of three amino acids, of which two exhibit "enantiomeric" main chain conformations. This simply means that the main chain torsion angles of the two adjacent amino acids are inverted about the centre of the Ramachandran plot. This results in the formation of "nests", which are defined as concave depressions which ultimately serve as binding sites.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>To determine the potential active sites of 2cfsA, the nest analysis method was utilized. Based on an article by Pal et. al, 2002, the principle of this method revolves around the possibility that anion (negatively-charged) and cation (positively-charged) binding sites in proteins are made up of three amino acids, of which two exhibit "enantiomeric" main chain conformations. This simply means that the main chain torsion angles of the two adjacent amino acids are inverted about the centre of the Ramachandran plot. This results in the formation of "nests", which are defined as concave depressions which ultimately serve as binding sites<ins style="font-weight: bold; text-decoration: none;">. Using the nest analysis method, 2oycA obtained similar results to that of 2cfsA. Keeping in mind that 2oycA is the PDB identifier for Chronophin, and that there is an article covering chronophin, it was used to identify potential structure-function relationships</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Visualizing the potential catalytic site of 2cfsA===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Visualizing the potential catalytic site of 2cfsA===</div></td></tr>
</table>Sitoh Kheng Waihttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10297&oldid=prevSitoh Kheng Wai: /* PDBsum */2008-06-09T16:44:33Z<p><span dir="auto"><span class="autocomment">PDBsum</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:44, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l90">Line 90:</td>
<td colspan="2" class="diff-lineno">Line 90:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The results obtained are significant as structural information is usually crucial for the functional prediction of the protein-of-interest. Since the information provided by the secondary structures of both proteins are highly similar, there is a great possibility that 2cfsA and 2oycA are functionally similar. <BR></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The results obtained are significant as structural information is usually crucial for the functional prediction of the protein-of-interest. Since the information provided by the secondary structures of both proteins are highly similar, there is a great possibility that 2cfsA and 2oycA are functionally similar. <BR></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2cfsA was identified to be from the haloacid dehalogenase-like hydrolase family (http://pfam.sanger.ac.uk/family?acc=PF00702). Members of this protein family (which includes phosphatases) belong to the Haloacid Dehalogenase (HAD) superfamily. Almo et al., 2007 mentions that members of the HAD superfamily catalyze phosphoryl transfer reactions in small molecules. It encompasses a large number of magnesium-dependent phosphohydrolases which are responsible for the co-ordination of the catalytically active magnesium ions, where the first aspartic acid serves as the nucleophile and phosphoryl acceptor. Further evidence highlighting the importance of the magnesium ions lie in the fact that when substituted with calcium, a near total loss of activity is observed. This highlights the significance of the magnesium ion, and also ties in with the work done using the ProFunc database, which predicts that 2cfsA is involved in catalytic processes.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2cfsA was identified to be from the haloacid dehalogenase-like hydrolase family (http://pfam.sanger.ac.uk/family?acc=PF00702). Members of this protein family (which includes phosphatases) belong to the Haloacid Dehalogenase (HAD) superfamily. Almo et al., 2007 mentions that members of the HAD superfamily catalyze phosphoryl transfer reactions in small molecules. It encompasses a large number of magnesium-dependent phosphohydrolases which are responsible for the co-ordination of the catalytically active magnesium ions, where the first aspartic acid serves as the nucleophile and phosphoryl acceptor. Further evidence highlighting the importance of the magnesium ions lie in the fact that when substituted with calcium, a near total loss of activity is observed. This highlights the significance of the magnesium ion, and also ties in with the work done using the ProFunc database, which predicts that 2cfsA is involved in catalytic processes<ins style="font-weight: bold; text-decoration: none;">. An assumption, therefore, would be that the magnesium ions are involved in the catalytic functions of 2cfsA</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===PROFUNC===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===PROFUNC===</div></td></tr>
</table>Sitoh Kheng Waihttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10295&oldid=prevSitoh Kheng Wai at 16:43, 9 June 20082008-06-09T16:43:24Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:43, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l105">Line 105:</td>
<td colspan="2" class="diff-lineno">Line 105:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Visualizing the potential catalytic site of 2cfsA===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Visualizing the potential catalytic site of 2cfsA===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Finally, a LIGPLOT of interactions involving the PLP ligand in 2cftA was obtained. The LIGPLOT was a good indication of the location of 2cftA's active site, highlighting the hydrogen bonds and non-bonded interactions between the ligand (in 2cfsA's case, the Magnesium ions) and the protein residues the ligand interacts with (Laskowski et al., 2001). It was also noticed that the Mg 1296(A) ion of 2cfsA was located in exactly the same position as 2cftA's calcium ion. This is significant as substitution of the Magnesium ion with the catalytically inert Calcium ion results in a loss of activity (Almo et al., 2007). Based on this, it was deduced that 2cfsA's active site is in the region surrounding Mg 1296(A). The LIGPLOT of interactions involving the Mg 1297(A) ion of 2cfsA was obtained, and this information - along with the information provided by the LIGPLOT involving the Mg 1296(A) - was used to generated a three-dimensional view of the catalytic site of 2cfsA via PyMOL. Compared to the earlier results based on the evolutionary aspect of the paper, the conserved regions - as obtained from the Multiple Sequence Alignment, was not too far off from the information (residues that constitute the catalytic site) obtained from Almo et al., 2007. PyMOL-generated visualizations of the possible catalytic sites using both sets of information illustrated this.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Finally, a LIGPLOT of interactions involving the PLP ligand in 2cftA was obtained. The LIGPLOT was a good indication of the location of 2cftA's active site, highlighting the hydrogen bonds and non-bonded interactions between the ligand (in 2cfsA's case, the Magnesium ions) and the protein residues the ligand interacts with (Laskowski et al., 2001). It was also noticed that the Mg 1296(A) ion of 2cfsA was located in exactly the same position as 2cftA's calcium ion. This is significant as substitution of the Magnesium ion with the catalytically inert Calcium ion results in a loss of activity (Almo et al., 2007). Based on this, it was deduced that 2cfsA's active site is in the region surrounding Mg 1296(A). The LIGPLOT of interactions involving the Mg 1297(A) ion of 2cfsA was obtained, and this information - along with the information provided by the LIGPLOT involving the Mg 1296(A) - was used to generated a three-dimensional view of the catalytic site of 2cfsA via PyMOL. Compared to the earlier results based on the evolutionary aspect of the paper, the conserved regions - as obtained from the Multiple Sequence Alignment, was not too far off from the information (residues that constitute the catalytic site) obtained from Almo et al., 2007. PyMOL-generated visualizations of the possible catalytic sites using both sets of information illustrated this.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">===Summary of Structure===</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">2cfsA belongs to the haloacid dehalogenase (HAD) superfamily, which catalyzes phosphoryl transfer reactions in small molecules. It encompasses a large number of magnesium-dependent phosphohydrolases which are responsible for the co-ordination of the catalytically active magnesium ions, where the first aspartic acid serves as the nucleophile and phosphoryl acceptor. Further evidence highlighting the importance of the magnesium ions lie in the fact that when substituted with calcium, a near total loss of activity is observed (Almo et al., 2007). This ties in with the work done using the ProFunc database, which predicts that 2cfsA is involved in catalytic processes.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td></tr>
</table>Sitoh Kheng Waihttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10294&oldid=prevSitoh Kheng Wai: /* PDBsum */2008-06-09T16:43:10Z<p><span dir="auto"><span class="autocomment">PDBsum</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:43, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l90">Line 90:</td>
<td colspan="2" class="diff-lineno">Line 90:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The results obtained are significant as structural information is usually crucial for the functional prediction of the protein-of-interest. Since the information provided by the secondary structures of both proteins are highly similar, there is a great possibility that 2cfsA and 2oycA are functionally similar. <BR></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The results obtained are significant as structural information is usually crucial for the functional prediction of the protein-of-interest. Since the information provided by the secondary structures of both proteins are highly similar, there is a great possibility that 2cfsA and 2oycA are functionally similar. <BR></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>2cfsA was identified to be from the haloacid dehalogenase-like hydrolase family (http://pfam.sanger.ac.uk/family?acc=PF00702). Members of this protein family (which includes phosphatases) belong to the Haloacid Dehalogenase (HAD) superfamily. Almo et al., 2007 mentions that the HAD superfamily encompasses a large number of magnesium-dependent phosphohydrolases <del style="font-weight: bold; text-decoration: none;">characterized by </del>a <del style="font-weight: bold; text-decoration: none;">DXDX motif - an indicator </del>of the catalytic <del style="font-weight: bold; text-decoration: none;">site</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>2cfsA was identified to be from the haloacid dehalogenase-like hydrolase family (http://pfam.sanger.ac.uk/family?acc=PF00702). Members of this protein family (which includes phosphatases) belong to the Haloacid Dehalogenase (HAD) superfamily. Almo et al., 2007 mentions that <ins style="font-weight: bold; text-decoration: none;">members of </ins>the HAD superfamily <ins style="font-weight: bold; text-decoration: none;">catalyze phosphoryl transfer reactions in small molecules. It </ins>encompasses a large number of magnesium-dependent phosphohydrolases <ins style="font-weight: bold; text-decoration: none;">which are responsible for the co-ordination of the catalytically active magnesium ions, where the first aspartic acid serves as the nucleophile and phosphoryl acceptor. Further evidence highlighting the importance of the magnesium ions lie in the fact that when substituted with calcium, </ins>a <ins style="font-weight: bold; text-decoration: none;">near total loss of activity is observed. This highlights the significance </ins>of the <ins style="font-weight: bold; text-decoration: none;">magnesium ion, and also ties in with the work done using the ProFunc database, which predicts that 2cfsA is involved in </ins>catalytic <ins style="font-weight: bold; text-decoration: none;">processes</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===PROFUNC===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===PROFUNC===</div></td></tr>
</table>Sitoh Kheng Waihttp://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Pyridoxal_Phosphatase_Discussion&diff=10290&oldid=prevSitoh Kheng Wai: /* Summary of Structure */2008-06-09T16:33:38Z<p><span dir="auto"><span class="autocomment">Summary of Structure</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:33, 9 June 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l107">Line 107:</td>
<td colspan="2" class="diff-lineno">Line 107:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Summary of Structure===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Summary of Structure===</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">2cfsA belongs to the haloacid dehalogenase (HAD) superfamily, which catalyzes phosphoryl transfer reactions in small molecules. It encompasses a large number of magnesium-dependent phosphohydrolases which are responsible for the co-ordination of the catalytically active magnesium ions, where the first aspartic acid serves as the nucleophile and phosphoryl acceptor. Further evidence highlighting the importance of the magnesium ions lie in the fact that when substituted with calcium, a near total loss of activity is observed (Almo et al., 2007). This ties in with the work done using the ProFunc database, which predicts that 2cfsA is involved in catalytic processes.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Function==</div></td></tr>
</table>Sitoh Kheng Wai