Sandbox 160: Difference between revisions

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Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH)has carefully been studied in a number of bacterial, parasitic and mammalian species and it has been found that it exists as homotetrameric protein <ref name="reference 1"/>. Each subunit within the protein is 38,151Da (tetramer is 152.4 kDa)and contains seven alpha helices and two beta sheets one of which has seven strands and the other with eight<ref name="reference 1"/> <ref name="ref 5">PMID:15953771</ref>. Two anion binding sites have been found where the two phosphates involved in the reaction will be bound during catalysis. One site is labeled "Pi" and is the location where the inorganic phosphate involved will bind and the other has been labeled "Ps" which is where the C-3 phosphate of Gylceraldeyhde 3-Phosphate will bind <ref name="reference 1"/>. Further experimentation has shown that the "Ps" site has been conserved in numerous GAPDH complexes and that the former may involve two possible sites in which the second or new "Pi" site is located 2.9 Angstroms from the primary "Pi" site<ref name="reference 1"/>.

The enzyme contains a functional NAD+ group which functions as a hydrogen acceptor during the course of the reaction which is bound to a Rossman fold. During the catalysis of glyceraldehyde 3-phosphate to 1,3-biphosphoglycerate a hydride ion is enzymatically transferred from the aldehyde group of glyceraldehyde 3-phosphate to the nicotinamide ring of NAD+ reducing it to NADH ~~(pink)~~<ref name="reference 1">PMID:19243605 </ref>. The active site of GAPDH contains a cysteine (Cys149 ~~colored green~~) residue which reacts with the glyceraldehyde 3-phosphate molecule through its -SH group. The substrate is covalently bound during the reaction through its aldehyde group to the -SH group of the cysteine residue and the resulting reaction produces a thiohemiacetal intermediate <ref name="reference 1"/>. Note that this reaction occurs through acid base catalysis with aid of a histidine residue (His176).The <scene name='Sandbox_160/Newscene/1'>active site</scene> of the molecule is illustrated to the right.

The enzyme contains a functional NAD+ group which functions as a hydrogen acceptor during the course of the reaction which is bound to a Rossman fold. During the catalysis of glyceraldehyde 3-phosphate to 1,3-biphosphoglycerate a hydride ion is enzymatically transferred from the aldehyde group of glyceraldehyde 3-phosphate to the nicotinamide ring of NAD+ reducing it to NADH<ref name="reference 1">PMID:19243605 </ref>. The active site of GAPDH contains a cysteine (Cys149) residue which reacts with the glyceraldehyde 3-phosphate molecule through its -SH group. The substrate is covalently bound during the reaction through its aldehyde group to the -SH group of the cysteine residue and the resulting reaction produces a thiohemiacetal intermediate <ref name="reference 1"/>. Note that this reaction occurs through acid base catalysis with aid of a histidine residue (His176).The <scene name='Sandbox_160/Newscene/1'>active site</scene> of the molecule is illustrated to the right.

A simplified illustration of the net reaction is as follows:

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== Active Site in Detail ==

[[Image:1vc2 image.png | left|thumb|upright=2 |Figure 1. Illustration created using PDB software highlighting the NAD+ ligand and Cysteine and Histidine residues within the active site of 1vc2.]] Once Glyceraldehyde 3-phophate comes into contact with the active site it forms a hydrogen bond through its C2 hydroxyl group to Cys149N. The C1 hydroxyl group of the substrate binds to His176NE2<ref name="ref 4">PMID:10191140 </ref>. Additional hydrogen bonds to the phosphate group of the substrate from additional residues such as Thr1790G1, Arg231NH1(these two residues are not highlighted in the illustration below) along with N7N and 02'N of the NAD+ moeity (pink) help stabilize the molecule during the course of the reaction in the active site <ref name="ref 4"/>. The nicotinamide ring of the NAD+ ligand is responsible for orienting the hydrogen atom at C1 towards itself which allows for easier transfer in producing in reducing NAD+ to NADH.

[[Image:1vc2 image.png | left|thumb|upright=2 |Figure 1. Illustration created using PDB software highlighting the NAD+ ligand and Cysteine and Histidine residues within the active site of 1vc2.]] Once Glyceraldehyde 3-phophate comes into contact with the active site it forms a hydrogen bond through its C2 hydroxyl group to Cys149N (Cys149 colored green. The C1 hydroxyl group of the substrate binds to His176NE2 (His176 colored teal)<ref name="ref 4">PMID:10191140 </ref>. Additional hydrogen bonds to the phosphate group of the substrate from additional residues such as Thr1790G1, Arg231NH1(these two residues are not highlighted in the illustration below) along with N7N and 02'N of the NAD+ moeity (NAD colored pink) help stabilize the molecule during the course of the reaction in the active site <ref name="ref 4"/>. The nicotinamide ring of the NAD+ ligand is responsible for orienting the hydrogen atom at C1 towards itself which allows for easier transfer in producing in reducing NAD+ to NADH.

==Relations to Medicine==

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@@ Line 11: / Line 11: @@
 Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH)has carefully been studied in a number of bacterial, parasitic and mammalian species and it has been found that it exists as homotetrameric protein <ref name="reference 1"/>. Each subunit within the protein is 38,151Da (tetramer is 152.4 kDa)and contains seven alpha helices and two beta sheets one of which has seven strands and the other with eight<ref name="reference 1"/> <ref name="ref 5">PMID:15953771</ref>. Two anion binding sites have been found where the two phosphates involved in the reaction will be bound during catalysis. One site is labeled "Pi" and is the location where the inorganic phosphate involved will bind and the other has been labeled "Ps" which is where the C-3 phosphate of Gylceraldeyhde 3-Phosphate will bind <ref name="reference 1"/>. Further experimentation has shown that the "Ps" site has been conserved in numerous GAPDH complexes and that the former may involve two possible sites in which the second or new "Pi" site is located 2.9 Angstroms from the primary "Pi" site<ref name="reference 1"/>.
-The enzyme contains a functional NAD+ group which functions as a hydrogen acceptor during the course of the reaction which is bound to a Rossman fold. During the catalysis of glyceraldehyde 3-phosphate to 1,3-biphosphoglycerate a hydride ion is enzymatically transferred from the aldehyde group of glyceraldehyde 3-phosphate to the nicotinamide ring of NAD+ reducing it to NADH (pink)<ref name="reference 1">PMID:19243605 </ref>. The active site of GAPDH contains a cysteine (Cys149 colored green) residue which reacts with the glyceraldehyde 3-phosphate molecule through its -SH group. The substrate is covalently bound during the reaction through its aldehyde group to the -SH group of the cysteine residue and the resulting reaction produces a thiohemiacetal intermediate <ref name="reference 1"/>. Note that this reaction occurs through acid base catalysis with aid of a histidine residue (His176).The <scene name='Sandbox_160/Newscene/1'>active site</scene> of the molecule is illustrated to the right.
+The enzyme contains a functional NAD+ group which functions as a hydrogen acceptor during the course of the reaction which is bound to a Rossman fold. During the catalysis of glyceraldehyde 3-phosphate to 1,3-biphosphoglycerate a hydride ion is enzymatically transferred from the aldehyde group of glyceraldehyde 3-phosphate to the nicotinamide ring of NAD+ reducing it to NADH<ref name="reference 1">PMID:19243605 </ref>. The active site of GAPDH contains a cysteine (Cys149) residue which reacts with the glyceraldehyde 3-phosphate molecule through its -SH group. The substrate is covalently bound during the reaction through its aldehyde group to the -SH group of the cysteine residue and the resulting reaction produces a thiohemiacetal intermediate <ref name="reference 1"/>. Note that this reaction occurs through acid base catalysis with aid of a histidine residue (His176).The <scene name='Sandbox_160/Newscene/1'>active site</scene> of the molecule is illustrated to the right.
 A simplified illustration of the net reaction is as follows:
@@ Line 24: / Line 24: @@
 == Active Site in Detail ==
-[[Image:1vc2 image.png | left|thumb|upright=2 |Figure 1. Illustration created using PDB software highlighting the NAD+ ligand and Cysteine and Histidine residues within the active site of 1vc2.]] Once Glyceraldehyde 3-phophate comes into contact with the active site it forms a hydrogen bond through its C2 hydroxyl group to Cys149N. The C1 hydroxyl group of the substrate binds to His176NE2<ref name="ref 4">PMID:10191140 </ref>. Additional hydrogen bonds to the phosphate group of the substrate from additional residues such as Thr1790G1, Arg231NH1(these two residues are not highlighted in the illustration below) along with N7N and 02'N of the NAD+ moeity (pink) help stabilize the molecule during the course of the reaction in the active site <ref name="ref 4"/>. The nicotinamide ring of the NAD+ ligand is responsible for orienting the hydrogen atom at C1 towards itself which allows for easier transfer in producing in reducing NAD+ to NADH.
+[[Image:1vc2 image.png | left|thumb|upright=2 |Figure 1. Illustration created using PDB software highlighting the NAD+ ligand and Cysteine and Histidine residues within the active site of 1vc2.]] Once Glyceraldehyde 3-phophate comes into contact with the active site it forms a hydrogen bond through its C2 hydroxyl group to Cys149N (Cys149 colored green. The C1 hydroxyl group of the substrate binds to His176NE2 (His176 colored teal)<ref name="ref 4">PMID:10191140 </ref>. Additional hydrogen bonds to the phosphate group of the substrate from additional residues such as Thr1790G1, Arg231NH1(these two residues are not highlighted in the illustration below) along with N7N and 02'N of the NAD+ moeity (NAD colored pink) help stabilize the molecule during the course of the reaction in the active site <ref name="ref 4"/>. The nicotinamide ring of the NAD+ ligand is responsible for orienting the hydrogen atom at C1 towards itself which allows for easier transfer in producing in reducing NAD+ to NADH.
 ==Relations to Medicine==