Sandbox 160: Difference between revisions

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D-glyceraldehyde 3-phosphate + phosphate + NAD+ ---------> 1,3 biphospho-D-glycerate + NADH + H+

The Pi that is involved in the reaction functions to attack by phosphorolysis the thioester intermediate that is formed by the substrate on the cysteine reside after NAD+ has been reduced <ref name="reference 1"/>. The attack by Pi on the carbonyl carbon of C1 is simultaneously followed by the replacement of bound NADH for NAD+ so another turn of the cycle can now commence. The final product is released as 1,3 bisphosphoglycerate in which the second Pi molecule has been incorporated.

The inorganic phosphate (Pi) that is involved in the reaction functions to attack by phosphorolysis the thioester intermediate that is formed by the substrate on the cysteine reside after NAD+ has been reduced <ref name="reference 1"/>. The attack by Pi on the carbonyl carbon of C1 is simultaneously followed by the replacement of bound NADH for NAD+ so another turn of the cycle can now commence. The final product is released as 1,3 bisphosphoglycerate in which the second Pi molecule has been incorporated.

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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 (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. The positive charge that arises when NADH is formed helps to stabilize the negatively charged oxygen on the carbonyl group that is present in the active site. Usually the holoenzyme form of GAPDH is found to contain NAD+ in two or three of its active sites, however in the protozoan parasite ''Cryptosporidium parvum'' NAD+ is found to be bound in each subunit<ref name="reference 1"/>. Binding of NAD+ to its designated subunit is known to cause a conformational change in that individual subunit and cause distances between residues to change. This is seen in ''E. coli'' in which it is known that upon the binding of NAD, the distance between the thiol group of the cysteine residue and the NE2 of the histidine atom increases within the active site<ref name="reference 1"/>. This movement and subsequent differences between residues in the active site or at other locations is thought to occur to support the NAD+ molecule and allow for hydrophobic interactions with the its ring<ref name="reference 1"/>. The movement of residues 77-83 in ''C. parvum'' maneuvers an important oxygen of residue K79 so that it is in favorable proximity to hydrogen bond with AN6 located on the ~~NAD+~~ molecule

[[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. The positive charge that arises when NADH is formed helps to stabilize the negatively charged oxygen on the carbonyl group that is present in the active site. Usually the holoenzyme form of GAPDH is found to contain NAD+ in two or three of its active sites, however in the protozoan parasite ''Cryptosporidium parvum'' NAD+ is found to be bound in each subunit<ref name="reference 1"/>. Binding of NAD+ to its designated subunit is known to cause a conformational change in that individual subunit and cause distances between residues to change. This is seen in ''E. coli'' in which it is known that upon the binding of the ligand (NAD+), the distance between the thiol group of the cysteine residue and the NE2 of the histidine atom increases within the active site<ref name="reference 1"/>. This movement and subsequent differences between residues in the active site or at other locations is thought to occur to support the NAD+ molecule and allow for hydrophobic interactions with the its ring<ref name="reference 1"/>. The movement of residues 77-83 in ''C. parvum'' maneuvers an important oxygen of residue K79 so that it is in favorable proximity to hydrogen bond with AN6 located on the ligand molecule.

==Relations to Medicine==

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@@ Line 17: / Line 17: @@
       D-glyceraldehyde 3-phosphate + phosphate + NAD+ ---------> 1,3 biphospho-D-glycerate + NADH + H+
-The Pi that is involved in the reaction functions to attack by phosphorolysis the thioester intermediate that is formed by the substrate on the cysteine reside after NAD+ has been reduced <ref name="reference 1"/>. The attack by Pi on the carbonyl carbon of C1 is simultaneously followed by the replacement of bound NADH for NAD+ so another turn of the cycle can now commence. The final product is released as 1,3 bisphosphoglycerate in which the second Pi molecule has been incorporated.
+The inorganic phosphate (Pi) that is involved in the reaction functions to attack by phosphorolysis the thioester intermediate that is formed by the substrate on the cysteine reside after NAD+ has been reduced <ref name="reference 1"/>. The attack by Pi on the carbonyl carbon of C1 is simultaneously followed by the replacement of bound NADH for NAD+ so another turn of the cycle can now commence. The final product is released as 1,3 bisphosphoglycerate in which the second Pi molecule has been incorporated.
@@ 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 (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. The positive charge that arises when NADH is formed helps to stabilize the negatively charged oxygen on the carbonyl group that is present in the active site. Usually the holoenzyme form of GAPDH is found to contain NAD+ in two or three of its active sites, however in the protozoan parasite ''Cryptosporidium parvum'' NAD+ is found to be bound in each subunit<ref name="reference 1"/>. Binding of NAD+ to its designated subunit is known to cause a conformational change in that individual subunit and cause distances between residues to change. This is seen in ''E. coli'' in which it is known that upon the binding of NAD, the distance between the thiol group of the cysteine residue and the NE2 of the histidine atom increases within the active site<ref name="reference 1"/>. This movement and subsequent differences between residues in the active site or at other locations is thought to occur to support the NAD+ molecule and allow for hydrophobic interactions with the its ring<ref name="reference 1"/>. The movement of residues 77-83 in ''C. parvum'' maneuvers an important oxygen of residue K79 so that it is in favorable proximity to hydrogen bond with AN6 located on the NAD+ molecule
+[[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. The positive charge that arises when NADH is formed helps to stabilize the negatively charged oxygen on the carbonyl group that is present in the active site. Usually the holoenzyme form of GAPDH is found to contain NAD+ in two or three of its active sites, however in the protozoan parasite ''Cryptosporidium parvum'' NAD+ is found to be bound in each subunit<ref name="reference 1"/>. Binding of NAD+ to its designated subunit is known to cause a conformational change in that individual subunit and cause distances between residues to change. This is seen in ''E. coli'' in which it is known that upon the binding of the ligand (NAD+), the distance between the thiol group of the cysteine residue and the NE2 of the histidine atom increases within the active site<ref name="reference 1"/>. This movement and subsequent differences between residues in the active site or at other locations is thought to occur to support the NAD+ molecule and allow for hydrophobic interactions with the its ring<ref name="reference 1"/>. The movement of residues 77-83 in ''C. parvum'' maneuvers an important oxygen of residue K79 so that it is in favorable proximity to hydrogen bond with AN6 located on the ligand molecule.
 ==Relations to Medicine==