https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Nathan+Line 2026-09-11T14:39:59Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1065047 2010-04-02T01:03:31Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/3'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/7'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/5'&gt;Histidine 178&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate. Though cystine-151 and histidine-178 are direct contributers to the catalytic process, other residues also influence the activity of this enzyme indirectly. &lt;scene name='Nathan_Line_sandbox_3/Other/2'&gt;Thr-210 and Arg-233&lt;/scene&gt; are two such residues that contribute to the binding of the reactants rather than the catalytic mechanism. Regulation of GAPDH occurs through its coupling with the PGK reaction. This coupling is needed due to the slightly positive delta G of the glycolysis. The larger negative delta G of the PGK reaction results in the following overall net reaction with a delta G of -12.1 kJ/mol:<br /> <br /> GAP + Pi + NAD+ + ADP ==&gt; 3PG + NADH + ATP<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html<br /> <br /> 3) &lt;ref group=&quot;xtra&quot;&gt;PMID:17676935&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 4) &lt;ref group=&quot;xtra&quot;&gt;PMID:7340828&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 5) &lt;ref group=&quot;xtra&quot;&gt;PMID:20164570&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1065046 2010-04-02T00:50:03Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/3'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/5'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/3'&gt;Histidine 178&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate. Though cystine-151 and histidine-178 are direct contributers to the catalytic process, other residues also influence the activity of this enzyme indirectly. &lt;scene name='Nathan_Line_sandbox_3/Other/1'&gt;Thr-210 and Arg-233&lt;/scene&gt; are two such residues that contribute to the binding of the reactants rather than the catalytic mechanism. Regulation of GAPDH occurs through its coupling with the PGK reaction. This coupling is needed due to the slightly positive delta G of the glycolysis. The larger negative delta G of the PGK reaction results in the following overall net reaction with a delta G of -12.1 kJ/mol:<br /> <br /> GAP + Pi + NAD+ + ADP ==&gt; 3PG + NADH + ATP<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html<br /> <br /> 3) &lt;ref group=&quot;xtra&quot;&gt;PMID:17676935&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 4) &lt;ref group=&quot;xtra&quot;&gt;PMID:7340828&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 5) &lt;ref group=&quot;xtra&quot;&gt;PMID:20164570&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1064749 2010-04-01T03:23:57Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/2'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/5'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/3'&gt;Histidine 178&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate. Though cystine-151 and histidine-178 are direct contributers to the catalytic process, other residues also influence the activity of this enzyme indirectly. &lt;scene name='Nathan_Line_sandbox_3/Other/1'&gt;Thr-210 and Arg-233&lt;/scene&gt; are two such residues that contribute to the binding of the reactants rather than the catalytic mechanism. Regulation of GAPDH occurs through its coupling with the PGK reaction. This coupling is needed due to the slightly positive delta G of the glycolysis. The larger negative delta G of the PGK reaction results in the following overall net reaction with a delta G of -12.1 kJ/mol:<br /> <br /> GAP + Pi + NAD+ + ADP ==&gt; 3PG + NADH + ATP<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html<br /> <br /> 3) &lt;ref group=&quot;xtra&quot;&gt;PMID:17676935&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 4) &lt;ref group=&quot;xtra&quot;&gt;PMID:7340828&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 5) &lt;ref group=&quot;xtra&quot;&gt;PMID:20164570&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1061802 2010-03-28T01:54:38Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/2'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/5'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/3'&gt;Histidine 178&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate. Though cystine-151 and histidine-178 are direct contributers to the catalytic process, other residues also influence the activity of this enzyme indirectly. &lt;scene name='Nathan_Line_sandbox_3/Other/1'&gt;Thr-210 and Arg-233&lt;/scene&gt; are two such residues that contribute to the binding of the reactants rather than the catalytic mechanism.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html<br /> <br /> 3) &lt;ref group=&quot;xtra&quot;&gt;PMID:17676935&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 4) &lt;ref group=&quot;xtra&quot;&gt;PMID:7340828&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;<br /> <br /> 5) &lt;ref group=&quot;xtra&quot;&gt;PMID:20164570&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1061800 2010-03-28T01:22:10Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/2'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/5'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/3'&gt;Histidine 178&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate. Though cystine-151 and histidine-178 are direct contributers to the catalytic process, other residues also influence the activity of this enzyme indirectly. &lt;scene name='Nathan_Line_sandbox_3/Other/1'&gt;Thr-210 and Arg-233&lt;/scene&gt; are two such residues that contribute to the binding of the reactants rather than the catalytic mechanism.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1061792 2010-03-28T00:41:28Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/2'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/5'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/3'&gt;Histidine 178&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate. Though cystine-151 and histidine-178 are direct contributers to the catalytic process, other residues also influence the activity of this enzyme. <br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1061776 2010-03-27T23:14:10Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/2'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/5'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/3'&gt;Histidine 178&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1061770 2010-03-27T22:54:45Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. Though each monomer does not have to exact same sequence, each does contain replicate active sites and function. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/2'&gt;active site&lt;/scene&gt; (highlighted in green), the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/5'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/2'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1061754 2010-03-27T21:15:17Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glycolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/1'&gt;active site&lt;/scene&gt;, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/4'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/2'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051064 2010-03-01T19:40:32Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/1'&gt;active site&lt;/scene&gt;, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/4'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/2'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051063 2010-03-01T19:40:11Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> GAP + NAD+ + Pi +GAPDH &lt;==&gt; 1,3-bisphosphoglycerate + NADH <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/1'&gt;active site&lt;/scene&gt;, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/4'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/2'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051060 2010-03-01T19:36:15Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/1'&gt;active site&lt;/scene&gt;, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/4'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/2'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain. Retrived from: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.c.b.d.html</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051055 2010-03-01T19:32:25Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/1'&gt;active site&lt;/scene&gt;, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/4'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/2'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> References:<br /> <br /> 1) Voet, D, Voet, J, &amp; Pratt, C. (2008). Fundamentals of biochemistry, third edition. Hoboken, NJ: Wiley &amp; Sons, Inc.<br /> <br /> 2)</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051030 2010-03-01T18:49:47Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/1'&gt;active site&lt;/scene&gt;, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/4'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/2'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051027 2010-03-01T18:45:59Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the &lt;scene name='Nathan_Line_sandbox_3/Active_site/1'&gt;active site&lt;/scene&gt;, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/3'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/1'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051023 2010-03-01T18:39:57Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel and antiparallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/3'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/1'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1051022 2010-03-01T18:38:37Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/3'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated &lt;scene name='Nathan_Line_sandbox_3/Histidine/1'&gt;Histidine 176&lt;/scene&gt; group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050740 2010-02-28T01:02:08Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/3'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated histidine group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050739 2010-02-28T01:00:01Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/2'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated histidine group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050737 2010-02-28T00:57:30Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl group from &lt;scene name='Nathan_Line_sandbox_3/Cystine/1'&gt;Cystine 151&lt;/scene&gt; attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated histidine group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050735 2010-02-28T00:45:25Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both &lt;scene name='Nathan_Line_sandbox_3/Secondary_structure/1'&gt;beta-sheets and alpha helixes&lt;/scene&gt;. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl groups attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated histidine group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050734 2010-02-28T00:38:52Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both beta-sheets and alpha helixes. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl groups attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated histidine group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050733 2010-02-28T00:38:13Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}<br /> <br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both beta-sheets and alpha helixes. This is consistent with the following SCOP information:<br /> <br /> Class: Alpha and beta proteins (a/b)<br /> <br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> <br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> <br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> <br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> <br /> Species: Human<br /> <br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl groups attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated histidine group. This produces the desired 1,3-bisphosphoglycerate.</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050732 2010-02-28T00:37:25Z

<p>Nathan Line: </p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a very important enzyme in the production of energy. This enzyme catalyzes the sixth step in the process of breaking down glucose into energy, also known as glycolysis. Though this is its main function, GAPDH has been shown to perform other functions including transcription activation, initiation of apoptosis, and ER to Golgi apparatus vesicle transportation. However, this page will focus on GAPDH’s role in glysolysis.<br /> GAPDH most commonly exists as what looks to be a dimer. Interesting though, the two monomers of the enzyme are not exactly the same. While one side consists only of parallel beta-sheets, the other monomer is made up of both beta-sheets and alpha helixes. This is consistent with the following SCOP information:<br /> Class: Alpha and beta proteins (a/b)<br /> Fold: NAD(P)-binding Rossmann-fold domains<br /> Superfamily: NAD(P)-binding Rossmann-fold domains<br /> Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminus domain<br /> Protein: Glyceraldehyde-3-phosphate dehydrogenase<br /> Species: Human<br /> The specific reaction that GAPDH catalyzes is shown below:<br /> <br /> The mechanism of the glycolysis reaction is fairly straight forward. After the aldehyde enters the active site, the sulfhydryl groups attacks the nucleophilic carbon to form a thiohemiacetal. This intermediate undergoes oxidation due to a hydride transfer to a nearby NAD+ forming a thioester. From here, a phosphate group enters and attacks the same carbonyl while at the same time it is separated from the cystine by the protonated histidine group. This produces the desired 1,3-bisphosphoglycerate.<br /> <br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=Glyceraldehyde-3-Phosphate_Dehydrogenase&diff=1050730 2010-02-27T23:53:05Z

<p>Nathan Line: New page: ==Glyceraldehyde-3-Phosphate Dehydrogenase== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click &quot;Show Preview&quot; at the bottom of t...</p> <hr /> <div>==Glyceraldehyde-3-Phosphate Dehydrogenase==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_3gpd | PDB=3gpd | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=Nathan_Line_sandbox_1&diff=1048774 2010-02-19T14:51:31Z

<p>Nathan Line: /* The Mechanism of Trypsin */</p> <hr /> <div>==The Mechanism of Trypsin==<br /> <br /> Trypsin is a serine protease that breaks down the backbone of peptides near positively charged side chains. [[2ah4]] The peptide is pulled into the active site by Asp 189. His 57 pulls on the hydrogen attached to the OH on Ser 195 to make it a better nucleophilie which attacks the carbonyl of the peptide. This tetrahedral intermediate removes the hydrogen from His 57 while the carbonyl reforms resulting in a break in the peptide backbone. After the amino group is replaced with water, the water again attacks the carbonyl and this tetrahedral collapses to reconstruct both the Ser195 and His57. The final products result in an amino group and a carboxylic acid compound. <br /> <br /> {{STRUCTURE_2ah4 | PDB=2ah4 | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=Nathan_Line_sandbox_1&diff=1048764 2010-02-19T14:50:17Z

<p>Nathan Line: /* The Mechanism of Trypsin */</p> <hr /> <div>==The Mechanism of Trypsin==<br /> <br /> Trypsin is a serine protease that breaks down the backbone of peptides near positively charged side chains. The peptide is pulled into the active site by Asp 189. His 57 pulls on the hydrogen attached to the OH on Ser 195 to make it a better nucleophilie which attacks the carbonyl of the peptide. This tetrahedral intermediate removes the hydrogen from His 57 while the carbonyl reforms resulting in a break in the peptide backbone. After the amino group is replaced with water, the water again attacks the carbonyl and this tetrahedral collapses to reconstruct both the Ser195 and His57. The final products result in an amino group and a carboxylic acid compound. <br /> <br /> {{STRUCTURE_2ah4 | PDB=2ah4 | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=Nathan_Line_sandbox_1&diff=1048738 2010-02-19T14:44:26Z

<p>Nathan Line: /* The Mechanism of Trypsin */</p> <hr /> <div>==The Mechanism of Trypsin==<br /> <br /> The peptide is pulled into the active site by Asp 189. His 57 pulls on the hydrogen attached to the OH on Ser 195 to make it a better nucleophilie which attacks the carbonyl of the peptide. This tetrahedral intermediate removes the hydrogen from His 57 while the carbonyl reforms resulting in a break in the peptide backbone. After the amino group is replaced with water, the water again attacks the carbonyl and this tetrahedral collapses to reconstruct both the Ser195 and His57. The final products result in an amino group and a carboxylic acid compound. <br /> <br /> {{STRUCTURE_2ah4 | PDB=2ah4 | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=Nathan_Line_sandbox_1&diff=1048737 2010-02-19T14:42:40Z

<p>Nathan Line: /* The Mechanism of Trypsin */</p> <hr /> <div>==The Mechanism of Trypsin==<br /> <br /> The peptide is pulled into the active site by Asp 189. His 57 pulls on the hydrogen attached to the OH on Ser 195 to make it a better nucleophilie which attacks the carbonyl of the peptide. This tetrahedral intermediate removes the hydrogen from His 57 while the carbonyl reforms resulting in a break in the peptide backbone. After the amino group is replaced with water, the water again attacks the carbonyl and this tetrahedral collapses to reconstruct both the Ser195 and His57. The final products result in an amino group and a carboxylic acid compound. <br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_3cin | PDB=3cin | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=Nathan_Line_sandbox_1&diff=1048736 2010-02-19T14:41:14Z

<p>Nathan Line: /* This is a placeholder */</p> <hr /> <div>==The Mechanism of Trypsin==<br /> <br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_3cin | PDB=3cin | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=Nathan_Line_sandbox_1&diff=1048733 2010-02-19T14:38:52Z

<p>Nathan Line: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click &quot;Show Preview&quot; at the bottom of this page to see how...</p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_3cin | PDB=3cin | SCENE= }}</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012804 2009-11-03T16:58:21Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide substrates [[http://images.google.com/imgres?imgurl=http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg&amp;imgrefurl=http://www.nature.com/nrc/journal/v7/n1/fig_tab/nrc2037_F1.html&amp;usg=__3dbY0r1Jy39GDzgNvA1BJ-PxgmU=&amp;h=362&amp;w=505&amp;sz=23&amp;hl=en&amp;start=5&amp;um=1&amp;tbnid=3OEbN1FJyVtexM:&amp;tbnh=93&amp;tbnw=130&amp;prev=/images%3Fq%3DPTEN%26hl%3Den%26rls%3DGGLJ,GGLJ:2006-34,GGLJ:en%26sa%3DN%26um%3D1|(1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.<br /> <br /> ===REFERENCES===<br /> <br /> &lt;ref group=&quot;xtra&quot;&gt;PMID:10555148&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012752 2009-11-03T14:47:43Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates [[http://images.google.com/imgres?imgurl=http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg&amp;imgrefurl=http://www.nature.com/nrc/journal/v7/n1/fig_tab/nrc2037_F1.html&amp;usg=__3dbY0r1Jy39GDzgNvA1BJ-PxgmU=&amp;h=362&amp;w=505&amp;sz=23&amp;hl=en&amp;start=5&amp;um=1&amp;tbnid=3OEbN1FJyVtexM:&amp;tbnh=93&amp;tbnw=130&amp;prev=/images%3Fq%3DPTEN%26hl%3Den%26rls%3DGGLJ,GGLJ:2006-34,GGLJ:en%26sa%3DN%26um%3D1|(1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.<br /> <br /> ===REFERENCES===<br /> <br /> &lt;ref group=&quot;xtra&quot;&gt;PMID:10555148&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012750 2009-11-03T14:46:31Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates [[http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg|(1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.<br /> <br /> ===REFERENCES===<br /> <br /> &lt;ref group=&quot;xtra&quot;&gt;PMID:10555148&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012749 2009-11-03T14:46:01Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates [[http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg|(1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.<br /> <br /> ===REFERENCES===<br /> <br /> &lt;ref group=&quot;xtra&quot;&gt;PMID:10555148&lt;/ref&gt;&lt;references group=&quot;xtra&quot;/&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012747 2009-11-03T14:44:21Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates [[http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg|(1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.<br /> <br /> ===REFERENCES===</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012745 2009-11-03T14:43:04Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates [[http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg|(1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012744 2009-11-03T14:42:39Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates [[http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg|(Figure 1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012742 2009-11-03T14:41:59Z

<p>Nathan Line: </p> <hr /> <div>{{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates [[http://www.nature.com/nrc/journal/v7/n1/images/nrc2037-f1.jpg|(Fig 1)]]. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012583 2009-11-02T17:10:50Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates (Fig 1). PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are two of the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012582 2009-11-02T17:09:57Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates (Fig 1). PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity. The last set of general mutations are involved in the interdomain hydrogen bonding the takes place between the two domains. Of the several amino acids that are incorporated into the hydrogen bonding, &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;Ser170 and Arg173&lt;/scene&gt; are among the eight most frequently mutated residues of PTEN. The severe decrease in phosphatase activity due to these mutations confirms the extreme importance of this interface for PTEN function.</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1012577 2009-11-02T16:26:34Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. This protein is a phosphatase that acts on both polypeptide and phosphoinositide sustrates (Fig 1). PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity.<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003345 2009-10-06T03:05:58Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln. There are several mutations located along some of the general portions of the protein. The most influencial of of these is the mutation of &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;Asp92&lt;/scene&gt; to Ala. This mutation alone causes a 700-fold reduction in the protein's catalytic activity.<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003344 2009-10-06T02:52:13Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop. In addition to the active loops in the phosphatase domain, the C2 domain also contains mutations that affect the protein's ability to interact with the membrane. This mutation is located at the &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;Leu345&lt;/scene&gt; which is mutated to a Gln.<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003343 2009-10-06T02:06:24Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop.<br /> <br /> &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003342 2009-10-06T02:05:51Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. The &quot;TI&quot; loop also contain mutations. These include mutations of &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;Thr167 and Gln171.&lt;/scene&gt; Though the Gln171 mutation is not directly inside the &quot;TI&quot; loop, its close proximity does affect the loop's function. These mutations decrease the activity by 60% and 75%. Even though this loop is not a part of the catalysis, its decreased interactions with the lipid hinders the catalytic reactions of the P-loop.<br /> <br /> &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003341 2009-10-06T01:43:02Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123&lt;/scene&gt;, which decrease the protein's activity from 50-60%. <br /> <br /> &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003335 2009-10-05T22:02:29Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> Mutations of PTEN occur within of the these different areas of the protein. The P-loop itself contains three mutations all of which decrease the protein's activity. This results in excessive cells growth and tumors. The amino acid mutated in the loop are &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;Lys125, Lys128, and His123.&lt;/scene&gt; <br /> <br /> &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003334 2009-10-05T21:50:30Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape. The other loop is the &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop.&lt;/scene&gt; This loop interacts with the lipid while in the active P-loop to increase the catalysis.<br /> <br /> &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line https://proteopedia.org/index.php?title=PTEN&diff=1003333 2009-10-05T21:46:28Z

<p>Nathan Line: </p> <hr /> <div>==This is a placeholder==<br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> &quot;Show Preview&quot; at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_1d5r | PDB=1d5r | SCENE=}}<br /> <br /> ===MUTATIONS OF PTEN IN CANCER===<br /> <br /> PTEN is a tumor suppressor protein that is mutated in several human cancers. These include glioblastomas, endometrial carcinomas, prostate carcinomas, and melanoma cases. PTEN has 403 amino acids which are separated into &lt;scene name='Nathan_Line_sandbox/Structure/6'&gt;two domains.&lt;/scene&gt; The red section represents the C2 domain which allows the protein to bind with phospholipid membrane. The phosphatase section (blue) interacts with the ligand and the phosphate head. These interactions are controled by two separate loops. The &lt;scene name='Nathan_Line_sandbox/Actice_site/1'&gt;P-loop&lt;/scene&gt; is responsible for the catalytic reactions performed by the protein. These reactions are what halt cell growth. The P-loop is made up of two parts, the catalytic parts (green) that perform the reactions and the conformational parts (purple) that force the loop into its conformational shape.<br /> <br /> <br /> <br /> &lt;scene name='Nathan_Line_sandbox/Structure/5'&gt;&quot;TI&quot; loop&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/P_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Ti_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/C2_mutations/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations1/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> &lt;scene name='Nathan_Line_sandbox/Other_mutations2/1'&gt;TextToBeDisplayed&lt;/scene&gt;</div>

Nathan Line