Sandbox 38
From Proteopedia
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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | ||
Like many proteins, the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/12'>secondary structure</scene> of adenylate kinase consists of two elements: alpha-helices (shown in light green) and beta-sheets (shown in dark green). Non-repetitive structural elements are shown in light blue/gray. In addition to the regular hydrogen bonding that causes the secondary structure of the protein, additional <scene name='Sandbox_38/Adenylate_kinase_2o_structure/15'>hydrogen bonding</scene> is present in the backbone of adenylate kinase (shown in yellow), which also contributes to the overall stability/folding of the molecule. | Like many proteins, the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/12'>secondary structure</scene> of adenylate kinase consists of two elements: alpha-helices (shown in light green) and beta-sheets (shown in dark green). Non-repetitive structural elements are shown in light blue/gray. In addition to the regular hydrogen bonding that causes the secondary structure of the protein, additional <scene name='Sandbox_38/Adenylate_kinase_2o_structure/15'>hydrogen bonding</scene> is present in the backbone of adenylate kinase (shown in yellow), which also contributes to the overall stability/folding of the molecule. | ||
| - | A additional, significant factor in the structural stability/folding of the molecule is the polarity of the amino acid residues. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/ | + | A additional, significant factor in the structural stability/folding of the molecule is the polarity of the amino acid residues. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/18'>hydrophobic</scene> (nonpolar) residues are shown in gray, while the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/17'>hydrophilic</scene> (polar/charged) residues are shown in red. |
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| + | ==Reactive structural elements== | ||
| + | As mentioned above, adenylate kinase catalyzes the reaction ATP + AMP = 2ADP. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/19'>catalytic residues</scene> that interact with the substrate to accomplish this are shown in purple. The amino acids that comprise these residues are Arg, Asp, and Lys. | ||
| + | However, the enzyme does not only interact with the ATP and AMP--it also interacts with <scene name='Sandbox_38/Adenylate_kinase_2o_structure/20'>Bis(adenosine)-5'-Pentaphosphate</scene> (shown in orange), a non-hydrolysable substrate with structural similarity to the enzyme's actual substrate. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/22'>contact residues</scene>, i.e. the residues that are in contact with the ligand, can be seen* (cationic residues are shown in blue, whereas anionic residues are shown in red). Similar to the catalytic residues, which have positively-charged side chains, the side chains that interact with the ligand are also primarily charged, although oxygen (primarily from Thr side chains) interacts with it as well. Furthermore, the carbonyl and nitrogen parts of the amino acid backbone also interact with the ligand. | ||
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| + | *The highlighted residues are actually those that are within 4 angstroms of the ligand, and all of them may not actually be in contact with it (although most of them are). | ||
==Water Accessibility== | ==Water Accessibility== | ||
The protein has certain <scene name='Sandbox_38/Adenylate_kinase_2o_structure/6'>water accessibility</scene> (water shown in blue, the enzyme shown in white), since water can't interact with all of it. Water also interacts with some of the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/7'>internal residues</scene>. Waters are and aren't places. | The protein has certain <scene name='Sandbox_38/Adenylate_kinase_2o_structure/6'>water accessibility</scene> (water shown in blue, the enzyme shown in white), since water can't interact with all of it. Water also interacts with some of the <scene name='Sandbox_38/Adenylate_kinase_2o_structure/7'>internal residues</scene>. Waters are and aren't places. | ||
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| - | ==Ligand== | ||
| - | Some <scene name='Sandbox_38/Adenylate_kinase_2o_structure/8'>residues contact the ligand</scene>. Although not all of the highlighted residues contact the ligand, most of them do. Cationic side chains are shown in blue, whereas anionic side chains are shown in red. What kind of side chains interact with non-hydrolysable substrate. The <scene name='Sandbox_38/Adenylate_kinase_2o_structure/10'>catalytic residues</scene> are shown in green. | ||
Revision as of 22:39, 19 October 2012
| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
is an enzyme that catalyzes the reaction ATP + AMP = 2ADP. It consists of two identical subunits, A (shown in blue) and B (shown in green). For simplicity's sake, only the A chain will be shown in consequent green links.
Basic structural elements
|
Like many proteins, the of adenylate kinase consists of two elements: alpha-helices (shown in light green) and beta-sheets (shown in dark green). Non-repetitive structural elements are shown in light blue/gray. In addition to the regular hydrogen bonding that causes the secondary structure of the protein, additional is present in the backbone of adenylate kinase (shown in yellow), which also contributes to the overall stability/folding of the molecule. A additional, significant factor in the structural stability/folding of the molecule is the polarity of the amino acid residues. The (nonpolar) residues are shown in gray, while the (polar/charged) residues are shown in red.
Reactive structural elements
As mentioned above, adenylate kinase catalyzes the reaction ATP + AMP = 2ADP. The that interact with the substrate to accomplish this are shown in purple. The amino acids that comprise these residues are Arg, Asp, and Lys. However, the enzyme does not only interact with the ATP and AMP--it also interacts with (shown in orange), a non-hydrolysable substrate with structural similarity to the enzyme's actual substrate. The , i.e. the residues that are in contact with the ligand, can be seen* (cationic residues are shown in blue, whereas anionic residues are shown in red). Similar to the catalytic residues, which have positively-charged side chains, the side chains that interact with the ligand are also primarily charged, although oxygen (primarily from Thr side chains) interacts with it as well. Furthermore, the carbonyl and nitrogen parts of the amino acid backbone also interact with the ligand.
- The highlighted residues are actually those that are within 4 angstroms of the ligand, and all of them may not actually be in contact with it (although most of them are).
Water Accessibility
The protein has certain (water shown in blue, the enzyme shown in white), since water can't interact with all of it. Water also interacts with some of the . Waters are and aren't places.
