Sandbox Reserved 1565: Difference between revisions

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The IMPDH <scene name='82/823089/Catalytic_triad/1'>catalytic triad</scene> includes Arg (325), Asn (306), and Asp (272). This is represented by the solid purple structures in the image. This triad is important as it makes cysteine more reactive as a nucleophilic component. This conserved cysteine, Cys334, (Cys331 in human type II IMPDH) induces binding after becoming more reactive.

<scene name='82/823089/Active_site/1'>~~Active Binding Site~~</scene> ~~The active binding site~~ includes the Bateman domains, which are components within the TIM barrel. Binding occurs after the catalytic triad makes cysteine more reactive. The cysteines that become more reactive are shown in green in the image, and are closely related to the active binding site. Asp259 (blue) hydrogen bonds with the ribose hydroxyls of NAD (nicotinamide region), and Ser315 (blue) hydrogen bonds to the ribose phosphate through hydroxyl groups. Gly361 and Gly383 (orange) have hydrophobic interactions with the phosphate of the ligand NAD. Other important interactions include Tyr403 hydrogen bonding to ribose phosphate (NAD), and Glu402 and Glu440 hydrogen bonding with the IMP purine ring.

The <scene name='82/823089/Active_site/1'>active binding site</scene> includes the Bateman domains, which are components within the TIM barrel. Binding occurs after the catalytic triad makes cysteine more reactive. The cysteines that become more reactive are shown in green in the image, and are closely related to the active binding site. Asp259 (blue) hydrogen bonds with the ribose hydroxyls of NAD (nicotinamide region), and Ser315 (blue) hydrogen bonds to the ribose phosphate through hydroxyl groups. Gly361 and Gly383 (orange) have hydrophobic interactions with the phosphate of the ligand NAD. Other important interactions include Tyr403 hydrogen bonding to ribose phosphate (NAD), and Glu402 and Glu440 hydrogen bonding with the IMP purine ring.

<scene name='82/823089/Charge_view/2'>~~IMPDH~~ charge</scene> is not strong, as shown by this view. There are positive and negative components within the structure, but a relatively neutral substance is better received in this mechanism due to a physiological environment. Negatively-charged glutamic acid and positively-charged histidine within this enzyme play a role within the covalent bindings in the mechanism. Covalent binding is necessary to form the covalent intermediate after NAD is reduced (after interacting with the active site residues).

IMPDH <scene name='82/823089/Charge_view/2'>charge</scene> is not positively or negatively strong as an entire protein, as shown by this view. There are positive and negative components within the structure, but a relatively neutral substance is better received in this mechanism due to a physiological environment. Negatively-charged glutamic acid and positively-charged histidine within this enzyme play a role within the covalent bindings in the mechanism. Covalent binding is necessary to form the covalent intermediate after NAD is reduced (after interacting with the active site residues).

<scene name='82/823089/Composition_view/1'>~~IMPDH~~ composition</scene> The dark pink RNA regions coincide with G5P and GDP ligands as they contain ribose groups. NAD, containing two ribose groups, (not pictured) is another ligand that is necessary in the hydrolysis of IMP in the mechanism. The green acetate ions are anions that function as ligands as as intermediate-step metabolites in the mechanism. Monocovalent cations travel through and activate IMPDH as anionic acetate ions buffer the system.

This enzyme's <scene name='82/823089/Composition_view/1'>composition</scene> contains mostly protein (brown) with no solvent. The dark pink RNA regions coincide with G5P and GDP ligands as they contain ribose groups. NAD, containing two ribose groups, (not pictured) is another ligand that is necessary in the hydrolysis of IMP in the mechanism. The green acetate ions are anions that function as ligands as as intermediate-step metabolites in the mechanism. Monocovalent cations travel through and activate IMPDH as anionic acetate ions buffer the system.

== Energy Transformation ==

Sandbox Reserved 1565: Difference between revisions

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 The IMPDH <scene name='82/823089/Catalytic_triad/1'>catalytic triad</scene> includes Arg (325), Asn (306), and Asp (272).  This is represented by the solid purple structures in the image. This triad is important as it makes cysteine more reactive as a nucleophilic component. This conserved cysteine, Cys334, (Cys331 in human type II IMPDH) induces binding after becoming more reactive.
-<scene name='82/823089/Active_site/1'>Active Binding Site</scene> The active binding site includes the Bateman domains, which are components within the TIM barrel. Binding occurs after the catalytic triad makes cysteine more reactive. The cysteines that become more reactive are shown in green in the image, and are closely related to the active binding site. Asp259 (blue) hydrogen bonds with the ribose hydroxyls of NAD (nicotinamide region), and Ser315 (blue) hydrogen bonds to the ribose phosphate through hydroxyl groups. Gly361 and Gly383 (orange) have hydrophobic interactions with the phosphate of the ligand NAD. Other important interactions include Tyr403 hydrogen bonding to ribose phosphate (NAD), and Glu402 and Glu440 hydrogen bonding with the IMP purine ring.
+The <scene name='82/823089/Active_site/1'>active binding site</scene> includes the Bateman domains, which are components within the TIM barrel. Binding occurs after the catalytic triad makes cysteine more reactive. The cysteines that become more reactive are shown in green in the image, and are closely related to the active binding site. Asp259 (blue) hydrogen bonds with the ribose hydroxyls of NAD (nicotinamide region), and Ser315 (blue) hydrogen bonds to the ribose phosphate through hydroxyl groups. Gly361 and Gly383 (orange) have hydrophobic interactions with the phosphate of the ligand NAD. Other important interactions include Tyr403 hydrogen bonding to ribose phosphate (NAD), and Glu402 and Glu440 hydrogen bonding with the IMP purine ring.
-<scene name='82/823089/Charge_view/2'>IMPDH charge</scene> is not strong, as shown by this view. There are positive and negative components within the structure, but a relatively neutral substance is better received in this mechanism due to a physiological environment. Negatively-charged glutamic acid and positively-charged histidine within this enzyme play a role within the covalent bindings in the mechanism. Covalent binding is necessary to form the covalent intermediate after NAD is reduced (after interacting with the active site residues).
+IMPDH <scene name='82/823089/Charge_view/2'>charge</scene> is not positively or negatively strong as an entire protein, as shown by this view. There are positive and negative components within the structure, but a relatively neutral substance is better received in this mechanism due to a physiological environment. Negatively-charged glutamic acid and positively-charged histidine within this enzyme play a role within the covalent bindings in the mechanism. Covalent binding is necessary to form the covalent intermediate after NAD is reduced (after interacting with the active site residues).
-<scene name='82/823089/Composition_view/1'>IMPDH composition</scene> The dark pink RNA regions coincide with G5P and GDP ligands as they contain ribose groups. NAD, containing two ribose groups, (not pictured) is another ligand that is necessary in the hydrolysis of IMP in the mechanism. The green acetate ions are anions that function as ligands as as intermediate-step metabolites in the mechanism. Monocovalent cations travel through and activate IMPDH as anionic acetate ions buffer the system.
+This enzyme's <scene name='82/823089/Composition_view/1'>composition</scene> contains mostly protein (brown) with no solvent. The dark pink RNA regions coincide with G5P and GDP ligands as they contain ribose groups. NAD, containing two ribose groups, (not pictured) is another ligand that is necessary in the hydrolysis of IMP in the mechanism. The green acetate ions are anions that function as ligands as as intermediate-step metabolites in the mechanism. Monocovalent cations travel through and activate IMPDH as anionic acetate ions buffer the system.
 == Energy Transformation ==