https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Michael+Nobbe 2026-09-15T19:31:58Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_2&diff=1084703 2010-05-07T20:34:16Z

<p>Michael Nobbe: Michael nobbe sandbox 2 moved to Isocitrate dehydrogenase: Ready for publication</p> <hr /> <div>#REDIRECT [[Isocitrate dehydrogenase]]</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1084702 2010-05-07T20:34:16Z

<p>Michael Nobbe: Michael nobbe sandbox 2 moved to Isocitrate dehydrogenase: Ready for publication</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha &lt;scene name='Michael_nobbe_sandbox_2/Alpha_beta_sandwich/1'&gt;sandwich structures.&lt;/scene&gt;. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mg2+ or Ca2+(&lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/4'&gt;Active Site&lt;/scene&gt;). This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved but they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mg+ ion next to the ligand which<br /> is surrounded by the residues of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1079450 2010-04-23T12:46:23Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha &lt;scene name='Michael_nobbe_sandbox_2/Alpha_beta_sandwich/1'&gt;sandwich structures.&lt;/scene&gt;. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mg2+ or Ca2+(&lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/4'&gt;Active Site&lt;/scene&gt;). This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved but they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mg+ ion next to the ligand which<br /> is surrounded by the residues of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1079449 2010-04-23T12:40:32Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha &lt;scene name='Michael_nobbe_sandbox_2/Alpha_beta_sandwich/1'&gt;sandwich structures.&lt;/scene&gt;. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+(&lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/4'&gt;Active Site&lt;/scene&gt;). This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved but they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mg+ ion next to the ligand which<br /> is surrounded by the residues of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1079448 2010-04-23T12:11:32Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha &lt;scene name='Michael_nobbe_sandbox_2/Alpha_beta_sandwich/1'&gt;sandwich structures.&lt;/scene&gt;. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+(&lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/4'&gt;Active Site&lt;/scene&gt;). This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved but they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residues of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1079442 2010-04-23T11:47:43Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha &lt;scene name='Michael_nobbe_sandbox_2/Alpha_beta_sandwich/1'&gt;sandwich structures.&lt;/scene&gt;. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+(&lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/4'&gt;Active Site&lt;/scene&gt;). This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved but they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1064798 2010-04-01T04:13:20Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha &lt;scene name='Michael_nobbe_sandbox_2/Alpha_beta_sandwich/1'&gt;sandwich structures.&lt;/scene&gt;. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+(&lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/4'&gt;Active Site&lt;/scene&gt;). This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1064777 2010-04-01T03:57:35Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+(&lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/4'&gt;Active Site&lt;/scene&gt;). This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1064775 2010-04-01T03:53:37Z

<p>Michael Nobbe: /* &#039;&#039;&#039;References&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''Inhibition'''==<br /> This step an irreversible reaction. It must be carefully regulated to avoid depletion of isocitrate in the body. The reaction is started by substrate availability which are: isocitrate,Mg2+, NAD+ or NADP+. If these are not present than the process will not carry forward. The reaction is inhibited by the removal of NADH from the presence of the citric acid cycle. The product is also inhibited by ATP feedback. This feedback inhibition is a competitive inhibitor. Since the citric acid cycle is used to produce energy molecules (ATP), an abundance of product will shut down the cycle.<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1064748 2010-04-01T03:23:05Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:Active site.jpg‎‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=File:Active_site.jpg&diff=1064746 2010-04-01T03:22:07Z

<p>Michael Nobbe: </p> <hr /> <div></div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1064743 2010-04-01T03:20:06Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1064741 2010-04-01T03:19:20Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which<br /> is surrounded by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1064718 2010-04-01T03:05:24Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Mechanism&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> is is better understood than the human mechanism. The &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Citrate Molecule&lt;/scene&gt; <br /> is converted to alpha-ketoglutarate. In the first step the alcohol group <br /> off the alpha-carbon is deprotonated by the Tyr residue. The electrons<br /> push to the oxygen atom to form a double bond (keytone). The remaining <br /> alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting <br /> cofactor. A carboxyl group pushes electrons down so an oxygen steals a <br /> nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic <br /> acid resulting in electron pushing that ejects a CO2. The two negatively <br /> charged oxygen's on the other side of the molecule are stabilized by the <br /> Mn2+. The double bond that was formed between the alpha and beta carbon <br /> removes a proton from the Tyr residue and the oxygen returns the a keytone <br /> and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> <br /> [[Image:Mechanism.jpg]] <br /> <br /> <br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059257 2010-03-24T04:14:23Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Mechanism&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygen's on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> [[Image:Mechanism.jpg]]<br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Ligand/2'&gt;Interactive Ligand&lt;/scene&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059254 2010-03-24T04:06:15Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Mechanism&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygen's on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> [[Image:Mechanism.jpg]]<br /> <br /> The mechanism by which isocitrate is converted to alpha-ketoglutarate &lt;ref&gt;http://en.wikipedia.org/wiki/File:IDHcatalyticmechanism.jpg&lt;/ref&gt;<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Ligand/1'&gt;Interactive Ligand&lt;/scene&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059252 2010-03-24T04:03:20Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Mechanism&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygen's on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Ligand/1'&gt;Interactive Ligand&lt;/scene&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059251 2010-03-24T04:02:02Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Tetra_active_site/1'&gt;Interactive Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygens on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below. <br /> <br /> <br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059249 2010-03-24T03:56:27Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.In human isocitrate dehydrogenase there are 4 subunits.<br /> <br /> <br /> {{STRUCTURE_1t0l | PDB=1t0l | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/2'&gt;Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygens on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below. <br /> <br /> <br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059247 2010-03-24T03:54:52Z

<p>Michael Nobbe: </p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=1to9 | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/2'&gt;Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygens on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below. <br /> <br /> <br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059243 2010-03-24T03:51:37Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Mechanism&#039;&#039;&#039; */</p> <hr /> <div>=='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons push to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygen's on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below.<br /> <br /> [[Image:Mechanism.jpg]]<br /> <br /> The mechanism of porcine isocitrate dehydrogenase<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Ligand/1'&gt;Interactive Ligand&lt;/scene&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=File:Mechanism.jpg&diff=1059232 2010-03-24T02:50:59Z

<p>Michael Nobbe: uploaded a new version of &quot;Image:Mechanism.jpg&quot;</p> <hr /> <div></div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059231 2010-03-24T02:50:01Z

<p>Michael Nobbe: /* &#039;&#039;&#039;References&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=1to9 | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/2'&gt;Active Site&lt;/scene&gt;<br /> <br /> =='''Function'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form&lt;ref&gt;PMID:15173171&lt;/ref&gt;. Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme &lt;ref&gt;PMID:15173171&lt;/ref&gt;. <br /> <br /> =='''Mechanism'''==<br /> The mechanism described is for porcine isocitrate dehydrogenase because is is better understood than the human mechanism. The alcohol group off the alpha-carbon is deprotonated by the Tyr residue. The electrons pust to the oxygen atom to form a double bond (keytone). The remaining alpha carbon hydrogen is removed using NAD+/NADP+ as an electron accepting cofactor. A carboxyl group pushes electrons down so an oxygen steals a nearby proton off a Lysine amino acid. The Tyr deprotanates the carboxylic acid resulting in electron pushing that ejects a CO2. The two negatively charged oxygens on the other side of the molecule are stabilized by the Mn2+. The double bond that was formed between the alpha and beta carbon removes a proton from the Tyr residue and the oxygen returns the a keytone and the alpha-ketoglutarate is formed. This is illustrated in the figure below. <br /> <br /> <br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059219 2010-03-24T02:12:49Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=1to9 | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/2'&gt;Active Site&lt;/scene&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059218 2010-03-24T02:10:53Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=3cin | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/2'&gt;Active Site&lt;/scene&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059217 2010-03-24T02:07:15Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=3cin | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> &lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/1'&gt;Isocitrate Active site&lt;/scene&gt;<br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059216 2010-03-24T02:04:34Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=3cin | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> &lt;scene name='Michael_nobbe_sandbox_2/Isocitrate_active_site/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059215 2010-03-24T02:00:08Z

<p>Michael Nobbe: /* &#039;&#039;&#039;The Active Site&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=3cin | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mn+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of similar properties and also are found in similar areas of the protein. Below is a picture of Porcine Active site with all of its residuals and ligands. <br /> <br /> <br /> [[Image:A.jpg‎]] <br /> <br /> The blue is the Mn+ ion next to the ligand which is surrounded<br /> by the residuals of that active site&lt;ref&gt;http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase#cite_note-nfr154197.2F32-6&lt;/ref&gt;.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> =='''References'''==<br /> <br /> <br /> &lt;references/&gt;</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059212 2010-03-24T01:33:45Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> <br /> {{STRUCTURE_1to9 | PDB=3cin | SCENE= }}<br /> <br /> =='''The Active Site'''==<br /> <br /> The active site of Isocitrate dehydrogenase binds the NAD+ or an NADP+ molecule as well as an Mg+ or Ca2+. This metal ion seems to be essential for catalysis&lt;ref&gt;PMID:15173171.&lt;/ref&gt;. Side chains of Asp 279 form hydrogen bonds with Ser94 (Human isocitrate dehydrogenase). Isocitrate is able to bind to the active site using about 8 amino acids like tyrosine, serine, asparagine, arginine, arginine, arginine, tyrosine, and lysine&lt;ref&gt;PMID:17632124.&lt;/ref&gt;. Across species these are not perfectly conserved by they are replaced with residues of</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059130 2010-03-23T16:44:52Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate 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_1to9 | PDB=3cin | SCENE= }}</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1059129 2010-03-23T16:37:47Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> [[Image:Human isocitrate.jpg]] [[Image:Chemicals isocitrate.jpg]]<br /> <br /> Human Isocitrate Dehydrogenase bound by NADH and CA2+ Citric Acid is converted to alpha-ketoglutarate<br /> and Citrate Image made using JMOL<br /> Image from: http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> [[Image:Active site isocitrate.jpg]]<br /> <br /> Active site of A chain. Human isocitrate dehydrogenase<br /> Image made using JMOL<br /> <br /> [[Image:E coli phosphorylation active site isocitrate.jpg]]<br /> <br /> Ecol i E coli isocitrate dehydrogenase after regulation by phosporylation of Ser94<br /> Image made using JMOL<br /> <br /> Works Cited<br /> <br /> PBD http://www.pdb.org/pdb/explore/explore.do;jsessionid=1701509E59152C072184587585E32ECD?structureId=1T09<br /> Jmol 1SJS, 1ICD, 1T09</div>

Michael Nobbe https://proteopedia.org/index.php?title=Isocitrate_dehydrogenase&diff=1059128 2010-03-23T16:15:48Z

<p>Michael Nobbe: New page: == &#039;&#039;&#039;Isocitrate Dehydrogenase&#039;&#039;&#039; == == &#039;&#039;&#039; Overview:&#039;&#039;&#039;== Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle ...</p> <hr /> <div>== '''Isocitrate Dehydrogenase''' ==<br /> == ''' Overview:'''==<br /> <br /> Isocitrate Dehydrogenase is an enzyme that is used during the third step of the [http://en.wikipedia.org/wiki/Citric_acid_cycle citric acid cycle]. This biological reaction is an essential process that is used to create molecules that are used for cellular energy. In this step it catalyzes the oxidative decarboxylation of isocitrate meaning that CO2 is released from the isocitrate. In addition coenzyme [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NAD]+ is converted to an [http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH]. This reaction results in an alpha-ketoglutarate molecule which is then moved on to the forth step of the citric acid cycle. <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate 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_3cin | PDB=3cin | SCENE= }}</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051119 2010-03-01T20:35:46Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> [[Image:Human isocitrate.jpg]] [[Image:Chemicals isocitrate.jpg]]<br /> <br /> Human Isocitrate Dehydrogenase bound by NADH and CA2+ Citric Acid is converted to alpha-ketoglutarate<br /> and Citrate Image made using JMOL<br /> Image from: http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> [[Image:Active site isocitrate.jpg]]<br /> <br /> Active site of A chain. Human isocitrate dehydrogenase<br /> Image made using JMOL<br /> <br /> [[Image:E coli phosphorylation active site isocitrate.jpg]]<br /> <br /> Ecol i E coli isocitrate dehydrogenase after regulation by phosporylation of Ser94<br /> Image made using JMOL<br /> <br /> Works Cited<br /> <br /> PBD http://www.pdb.org/pdb/explore/explore.do;jsessionid=1701509E59152C072184587585E32ECD?structureId=1T09<br /> Jmol 1SJS, 1ICD, 1T09</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051118 2010-03-01T20:34:32Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Function:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> [[Image:Human isocitrate.jpg]]<br /> <br /> Human Isocitrate Dehydrogenase bound by NADH and CA2+<br /> and Citrate<br /> Image made using JMOL<br /> <br /> [[Image:Chemicals isocitrate.jpg]]<br /> <br /> Citric Acid is converted to alpha-ketoglutarate<br /> <br /> Image from: http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> [[Image:Active site isocitrate.jpg]]<br /> <br /> Active site of A chain. Human isocitrate dehydrogenase<br /> Image made using JMOL<br /> <br /> [[Image:E coli phosphorylation active site isocitrate.jpg]]<br /> <br /> Ecol i E coli isocitrate dehydrogenase after regulation by phosporylation of Ser94<br /> Image made using JMOL<br /> <br /> Works Cited<br /> <br /> PBD http://www.pdb.org/pdb/explore/explore.do;jsessionid=1701509E59152C072184587585E32ECD?structureId=1T09<br /> Jmol 1SJS, 1ICD, 1T09</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051117 2010-03-01T20:32:03Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Function:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> [[Image:Human isocitrate.jpg]]<br /> <br /> Human Isocitrate Dehydrogenase bound by NADH and CA2+<br /> and Citrate<br /> Image made using JMOL<br /> <br /> [[Image:Chemicals isocitrate.jpg]]<br /> <br /> Citric Acid is converted to alpha-ketoglutarate<br /> <br /> Image from: http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> [[Image:Active site isocitrate.jpg]]<br /> <br /> Active site of A chain. Human isocitrate dehydrogenase<br /> Image made using JMOL<br /> <br /> [[Image:E coli phosphorylation active site isocitrate.jpg]]<br /> <br /> Ecol i E coli isocitrate dehydrogenase after regulation by phosporylation of Ser94<br /> Image made using JMOL</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051112 2010-03-01T20:27:46Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> [[Image:Human isocitrate.jpg]]<br /> <br /> Human Isocitrate Dehydrogenase bound by NADH and CA2+<br /> and Citrate<br /> Image made using JMOL<br /> <br /> [[Image:Chemicals isocitrate.jpg]]<br /> <br /> Citric Acid is converted to alpha-ketoglutarate<br /> <br /> Image from: http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> [[Image:c:/.jpg]]</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051110 2010-03-01T20:27:03Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> [[Image:Human isocitrate.jpeg]]<br /> <br /> Human Isocitrate Dehydrogenase bound by NADH and CA2+<br /> and Citrate<br /> Image made using JMOL<br /> <br /> [[Image:Chemicals isocitrate.jpeg]]<br /> <br /> Citric Acid is converted to alpha-ketoglutarate<br /> <br /> Image from: http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> [[Image:c:/.jpg]]</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051109 2010-03-01T20:26:11Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> [[Image:Human isocitrate]]<br /> <br /> Human Isocitrate Dehydrogenase bound by NADH and CA2+<br /> and Citrate<br /> Image made using JMOL<br /> <br /> [[Image:Chemicals isocitrate]]<br /> <br /> Citric Acid is converted to alpha-ketoglutarate<br /> <br /> Image from: http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> [[Image:c:/.jpg]]</div>

Michael Nobbe https://proteopedia.org/index.php?title=File:Human_isocitrate.jpg&diff=1051106 2010-03-01T20:21:19Z

<p>Michael Nobbe: </p> <hr /> <div></div>

Michael Nobbe https://proteopedia.org/index.php?title=File:E_coli_phosphorylation_active_site_isocitrate.jpg&diff=1051105 2010-03-01T20:20:59Z

<p>Michael Nobbe: </p> <hr /> <div></div>

Michael Nobbe https://proteopedia.org/index.php?title=File:Chemicals_isocitrate.jpg&diff=1051104 2010-03-01T20:20:40Z

<p>Michael Nobbe: </p> <hr /> <div></div>

Michael Nobbe https://proteopedia.org/index.php?title=File:Active_site_isocitrate.jpg&diff=1051103 2010-03-01T20:20:25Z

<p>Michael Nobbe: </p> <hr /> <div></div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051101 2010-03-01T20:18:37Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Function:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase<br /> [[Image:c:/.jpg]]</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051096 2010-03-01T20:11:50Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Function:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> <br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051095 2010-03-01T20:11:25Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Function:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).<br /> <br /> <br /> [[Image:a.jpg ]]<br /> Image from:http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051092 2010-03-01T20:10:22Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051090 2010-03-01T20:09:47Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> [[Image:a.jpg ]]<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).</div>

Michael Nobbe https://proteopedia.org/index.php?title=File:A.jpg&diff=1051089 2010-03-01T20:09:01Z

<p>Michael Nobbe: uploaded a new version of &quot;Image:A.jpg&quot;</p> <hr /> <div></div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051087 2010-03-01T20:08:00Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> [[Image:C:\Users\Nobbe\Desktop\a.jpg ]]<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).</div>

Michael Nobbe https://proteopedia.org/index.php?title=Michael_nobbe_sandbox_1&diff=1051083 2010-03-01T20:05:57Z

<p>Michael Nobbe: /* &#039;&#039;&#039;Structure:&#039;&#039;&#039; */</p> <hr /> <div>== '''Isocitrate dehydrogenase''' ==<br /> <br /> <br /> <br /> <br /> <br /> == '''Structure:'''==<br /> <br /> Isocitrate dehydrogenase is SCOP classified as an alpha beta structure. Its secondary composition consists of mainly alpha helices and beta sheets which are arranged into three layer alpha beta alpha sandwich structures. The entire protein consists of two side by side sandwich structures that face opposite directions. This then causes the proteins two active sites to face opposite directions as well. These two groups make up the A and B subunits of isocitrate dehydrogenase.<br /> [[Image: ]]<br /> <br /> == '''Function:'''==<br /> <br /> Isocitrate dehydrogenase is a digestive enzyme that is used in the citric acid cycle. Its main function is to catalyze the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. Human isocitrate dehydrogenase is regulation is not fully understood however, it is known that NADP and Ca2+ bind in the active site to create three different conformations. These conformations form in the active site and are as follows: a loop is form in the inactive enzyme, a partially unraveled alpha helix in the semi open form, and a alpha helix in the active form (PDB). Bacterial isocitrate dehydrogenase uses phosphorylation for regulation. The Ser94 residue undergoes reversible phosphorylation causing structural changes in the active site which hinders the catalytic function of the enzyme (PBD).</div>

Michael Nobbe