Sandbox 36
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| - | <Structure load=' | + | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> |
| + | <Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Sandbox_36/Adenylate_kinase/4' /> | ||
| + | =Background= | ||
| + | Adenylate kinase is an important protein found within the bacterium, Yersinia pestis, the culprit of the bubonic plagues. According to Relationship between bacterial virulence and nucleotide metabolism: a mutation in the adenylate kinase gene renders Yersinia pestis avirulent, by Munier-Lehmann H et al., a mutant form of adenylate kinase was able to be digested and was unable to infect mice. <scene name='Sandbox_36/Adenylate_kinase/4'>Adenylate kinase</scene> is a phosphotransferase protein, that catalyzes the reaction of adenosine triphosphate (ATP) and adenosine monophosphate (AMP), to form two molecules of adenosine diphosphate (ADP). | ||
| + | =Structure= | ||
| + | In the <scene name='Sandbox_36/Crystal_structure/1'>crystal structure</scene>, adenylate kinase dimerizes because of interactions with another molecule of adenylate kinase, that are not existent within a living organism. It is actually comprised of just one <scene name='Sandbox_36/Rainbow_map/1'>amino acid chain</scene>, which is highlighted from N-terminus to C-terminus, blue to red, respectively. | ||
| - | ==''' | + | Adenylate kinase's <scene name='Sandbox_36/Secondary_structure_of_ak/1'>secondary structural characteristics</scene> consist of twelve (12) alpha helices, shown in brown, and seven (7) beta sheets, shown in blue. <scene name='Sandbox_36/The_bonds_of_backbone/1'>Hydrogen bonds</scene>, shown as black, dashed lines, hold together the secondary structural features of adenylate kinase. Most of the beta sheets, in this protein, are aligned parallel to one another. This is evident by the presence of an angle of the hydrogen bonds between the sheets; antiparallel sheets have parallel hydrogen bonding. |
| + | =Interactions= | ||
| + | Here the <scene name='Sandbox_36/Hydrophobic_residues_alone/1'>hydrophobic</scene> residues are pictured in light grey, and in this scene the <scene name='Sandbox_36/Charged_and_polar/1'>hydrophilic</scene> (charged, polar) residues are pictured in brown. In this representation both the <scene name='Sandbox_36/Residues_together/1'>hydrophobic and hydrophilic</scene> residues are shown in the same colors as previously. It can be seen that there is a cleft in the protein, which is lined with hydrophilic residues. This is most likely the area in which the substrates and/or ligand enter into the active site. It can also be noted that both hydrophobic and hydrophilic residues come in contact with the ligand, which is expected. | ||
| - | = | + | Here the <scene name='Sandbox_36/Water/1'>solvent</scene>, represented by dark grey spheres, is displayed. The placement of the solvent molecules help to confirm the prediction of the location of entry for substrates and ligands, in the cleft. The solvent is mainly on the exterior of the protein; it cannot be found in the "spaces" of the protein. This is because there actually are not any "spaces" the solvent to fit into the protein, as can be seen in this <scene name='Sandbox_36/Adenylate_kinase_space_fill/1'>space filling</scene> model of adenylate kinase. |
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| - | + | In this scene, the interactions between the <scene name='Sandbox_36/Ligand_interactions/1'>residues and ligand</scene> are represented. Anionic side chains are red, cationic side chains are blue, and histidine residues are light blue. Most of the residues that interact with the ligand are cationic, or positive, which makes sense because the ligand contains many negatively charged phosphate groups. The <scene name='Sandbox_36/Catalytic_residues/1'>catalytic residues</scene>, pictured in brown, are focused towards the center of the ligand. This also matches the data, as the purpose of adenylate kinase is to transfer a phosphate group from ATP to AMP. | |
| - | + | =Resources= | |
| + | [http://www.ncbi.nlm.nih.gov/pubmed www.ncbi.nlm.nih.gov/pubmed] | ||
| - | + | [http://www.ebi.ac.uk/pdbsum/ www.ebi.ac.uk/pdbsum/] | |
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| - | + | [http://www.wikipedia.org/ www.wikipedia.org/] | |
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Current revision
| 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. |
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Contents |
Background
Adenylate kinase is an important protein found within the bacterium, Yersinia pestis, the culprit of the bubonic plagues. According to Relationship between bacterial virulence and nucleotide metabolism: a mutation in the adenylate kinase gene renders Yersinia pestis avirulent, by Munier-Lehmann H et al., a mutant form of adenylate kinase was able to be digested and was unable to infect mice. is a phosphotransferase protein, that catalyzes the reaction of adenosine triphosphate (ATP) and adenosine monophosphate (AMP), to form two molecules of adenosine diphosphate (ADP).
Structure
In the , adenylate kinase dimerizes because of interactions with another molecule of adenylate kinase, that are not existent within a living organism. It is actually comprised of just one , which is highlighted from N-terminus to C-terminus, blue to red, respectively.
Adenylate kinase's consist of twelve (12) alpha helices, shown in brown, and seven (7) beta sheets, shown in blue. , shown as black, dashed lines, hold together the secondary structural features of adenylate kinase. Most of the beta sheets, in this protein, are aligned parallel to one another. This is evident by the presence of an angle of the hydrogen bonds between the sheets; antiparallel sheets have parallel hydrogen bonding.
Interactions
Here the residues are pictured in light grey, and in this scene the (charged, polar) residues are pictured in brown. In this representation both the residues are shown in the same colors as previously. It can be seen that there is a cleft in the protein, which is lined with hydrophilic residues. This is most likely the area in which the substrates and/or ligand enter into the active site. It can also be noted that both hydrophobic and hydrophilic residues come in contact with the ligand, which is expected.
Here the , represented by dark grey spheres, is displayed. The placement of the solvent molecules help to confirm the prediction of the location of entry for substrates and ligands, in the cleft. The solvent is mainly on the exterior of the protein; it cannot be found in the "spaces" of the protein. This is because there actually are not any "spaces" the solvent to fit into the protein, as can be seen in this model of adenylate kinase.
In this scene, the interactions between the are represented. Anionic side chains are red, cationic side chains are blue, and histidine residues are light blue. Most of the residues that interact with the ligand are cationic, or positive, which makes sense because the ligand contains many negatively charged phosphate groups. The , pictured in brown, are focused towards the center of the ligand. This also matches the data, as the purpose of adenylate kinase is to transfer a phosphate group from ATP to AMP.
