Sandbox 33: Difference between revisions

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==Adenylate Kinase==

<scene name='Sandbox_33/1ake/1'>Adenylate kinase</scene> (also known as 1AKE) is an enzyme that performs a reaction that quickly converts ATP to ADP. Adenylate Kinase thus plays an important role in cellular metabolism. The images of Adenylate Kinase in this sandbox are from Yersinia Pestis~~, which is commonly called yeast~~.

<scene name='Sandbox_33/1ake/1'>Adenylate kinase</scene> (also known as 1AKE) is an enzyme that performs a reaction that quickly converts ATP to ADP. Adenylate Kinase thus plays an important role in cellular metabolism. The images of Adenylate Kinase in this sandbox are from Yersinia Pestis.

==Secondary Structure==

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==Enzyme Activity==

~~DONT FORGET: When you add the green link to the top part of the page, make sure you say something about what kinds of side-chains interact with the non-hydrolysable substrate, and if that makes sense.~~

The active site is where the substrate binds to the enzyme to be catalyzed. The ligand binds to the <scene name='Sandbox_33/Ligand_contacts/1'>ligand contacts</scene> (depicted in color) of the protein. There are mostly hydrophilic residues in the active site because water enter the active site. There are also some hydrophobic residues in the active site, which interacts with the hydrophobic portions of the substrate (or more likely, the transition state) to stabilize it during catalysis. There are six <scene name='Sandbox_33/Catalytic_residues/1'>catalytic residues</scene> (which are highlighted in blue while all the ligand contacts are depicted in pink) which help perform the catalysis by forming hydrogen bonds with the substrate to hold it in place for the reaction.

The active site is where the substrate binds to the enzyme to be catalyzed. The ligand binds to the <scene name='Sandbox_33/Ligand_contacts/1'>ligand contacts</scene> (depicted in color) of the protein. There are mostly hydrophilic ~~residue~~ in the active site because water enter the active site. ~~As previously mentioned, there~~ are some hydrophobic ~~interactions~~ in the active site, which interacts with the hydrophobic portions of the substrate (or more likely, the transition state) to stabilize it during catalysis. There are ~~SIX~~ <scene name='Sandbox_33/Catalytic_residues/1'>catalytic residues</scene> ~~CHECK TO SEE IF RIGHT ONES~~ which are highlighted in blue while all the ligand contacts are depicted in pink, which help perform the catalysis by forming hydrogen bonds with the substrate to hold it in place for the reaction. The catalytic residues are all charged residues, including lysinE, aspartic acid, and arginine. These residues also allow for electrostatic interactions but can be effected by water in the active site.

==Resources==

http://en.wikipedia.org/wiki/Adenylate_kinase

Sandbox 33: Difference between revisions

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@@ Line 5: / Line 5: @@
 ==Adenylate Kinase==
-<scene name='Sandbox_33/1ake/1'>Adenylate kinase</scene> (also known as 1AKE) is an enzyme that performs a reaction that quickly converts ATP to ADP. Adenylate Kinase thus plays an important role in cellular metabolism.  The images of Adenylate Kinase in this sandbox are from Yersinia Pestis, which is commonly called yeast.
+<scene name='Sandbox_33/1ake/1'>Adenylate kinase</scene> (also known as 1AKE) is an enzyme that performs a reaction that quickly converts ATP to ADP. Adenylate Kinase thus plays an important role in cellular metabolism.  The images of Adenylate Kinase in this sandbox are from Yersinia Pestis.
 ==Secondary Structure==
@@ Line 23: / Line 23: @@
 ==Enzyme Activity==
-DONT FORGET: When you add the green link to the top part of the page, make sure you say something about what kinds of side-chains interact with the non-hydrolysable substrate, and if that makes sense.
+The active site is where the substrate binds to the enzyme to be catalyzed. The ligand binds to the <scene name='Sandbox_33/Ligand_contacts/1'>ligand contacts</scene> (depicted in color) of the protein.  There are mostly hydrophilic residues in the active site because water enter the active site.  There are also some hydrophobic residues in the active site, which interacts with the hydrophobic portions of the substrate (or more likely, the transition state) to stabilize it during catalysis.  There are six <scene name='Sandbox_33/Catalytic_residues/1'>catalytic residues</scene> (which are highlighted in blue while all the ligand contacts are depicted in pink) which help perform the catalysis by forming hydrogen bonds with the substrate to hold it in place for the reaction.
-The active site is where the substrate binds to the enzyme to be catalyzed. The ligand binds to the <scene name='Sandbox_33/Ligand_contacts/1'>ligand contacts</scene> (depicted in color) of the protein.  There are mostly hydrophilic residue in the active site because water enter the active site.  As previously mentioned, there are some hydrophobic interactions in the active site, which interacts with the hydrophobic portions of the substrate (or more likely, the transition state) to stabilize it during catalysis.  There are SIX <scene name='Sandbox_33/Catalytic_residues/1'>catalytic residues</scene>  CHECK TO SEE IF RIGHT ONES which are highlighted in blue while all the ligand contacts are depicted in pink, which help perform the catalysis by forming hydrogen bonds with the substrate to hold it in place for the reaction.  The catalytic residues are all charged residues, including lysinE, aspartic acid, and arginine.  These residues also allow for electrostatic interactions but can be effected by water in the active site.
 ==Resources==
 http://en.wikipedia.org/wiki/Adenylate_kinase