Sandbox 48
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| - | {{Template: | + | <!-- PLEASE DO NOT DELETE THIS TEMPLATE --> |
| + | {{Template:Oberholser_Sandbox_Reservation}} | ||
| + | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
| + | <Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | ||
| - | == General Preliminary Information and Historical Development == | ||
| - | Lysozyme is an enzyme known for its unique ability to degrade the polysaccharide architecture of many kinds of cell walls, normally for the purpose of protection against bacterial infection<ref>Lysozyme. 2010. Citizendium.org. http://en.citizendium.org/wiki/Lysozyme</ref>. In avian species, lysozyme is an abundant component of egg white, in which lysozyme functions as an antibiotic and as a nutrient for early embryogenesis <ref>Sears, D.W. 2010. Overview of the Structure and Function of Hen Egg-White Lysozyme. Ucsb.edu. http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm/</ref>. In vertebrate species, lysozyme is generally found in mucosal secretions, such as tears and saliva, and functions in the same way that it functions in avian species for antibacterial purposes. | ||
| - | + | == Adenylate Kinase == | |
| - | == General Function == | ||
| - | Lysozyme is a 129 amino acid-long enzyme that is particularly specific in its cleavage proclivity for alternating polysaccharide copolymers of N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM), which architectural theme represents the "unit" polysaccharide structure of many bacterial cell walls <ref>Sears, D.W. 2010. Overview of the Structure and Function of Hen Egg-White Lysozyme. Ucsb.edu. http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-enz/lysozyme/HEWL/lysozyme-overview.htm/</ref>. The location of cleavage for lysozyme on this architectural theme is the β(1-4) glycosidic linkage connecting connecting the C1 carbon of NAM to the C4 carbon of NAG. The particular substrate of preference for this cleavage type is a (NAG-NAM)₃ hexasaccharide, within which substrate occurs the cleaving target glycosidic bond of NAM₄-β-O-NAG₅. The individual hexasaccharide binding units are designated A-F, with the NAM₄-β-O-NAG₅ glycosidic bond cleavage preference corresponding to a D-E unit glycosidic bond cleavage preference. | ||
| + | <scene name='Sandbox_48/Full_adenylate_kinase/1'>Adenylate kinase</scene> (or ADK) is an enzyme known to catalyze the reversible interconversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to two molecules of adenosine diphosphate (ADP). | ||
| - | < | + | Reaction Scheme: ATP + AMP ⇔ 2 ADP |
| + | |||
| + | This enzyme is important for cellular energy homeostasis because the need for ADP. ADP is required for oxidative phosphorylation, an important step in multiple metabolic pathways. | ||
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| + | == Secondary Structure & Hydrogen Bonds == | ||
| + | The structure of <scene name='Sandbox_48/Adenylate_kinase__chain_a/1'>chain A in adenylate kinase</scene> demonstrates the types of secondary structure that make up the enzyme. | ||
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| + | The <scene name='Sandbox_48/Secondary__structure__greenblu/4'>secondary structures</scene> of chain A of adenylate kinase includes alpha- | ||
| + | <scene name='Sandbox_48/Secondary__structure__helix/1'>helices</scene> (green), and <scene name='Sandbox_48/Secondary__structure__betashee/1'>beta sheets</scene> (blue). There are 12 total helices in the enzyme, and 2 types of | ||
| + | beta sheets, a parallel with 5 strands and an antiparallel with 2 strands. The location of the <scene name='Sandbox_48/2_structure_hbondson/1'>hydrogen bonds</scene> (black) within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded. | ||
| + | |||
| + | == Hydrophobic and Hydrophilic Residues == | ||
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| + | Within these structures the <scene name='Sandbox_48/Secondary__structure__hydropho/1'>hydrophobic</scene> residues (purple) are located closest on the inside of the enzyme. The <scene name='Sandbox_48/Secondary__structure__hydrophi/1'>hydrophillic </scene> residues (green), which are those that are charged or polar, are on the outward face of the enzyme. | ||
| + | |||
| + | == Solvent Accessibility == | ||
| + | |||
| + | In the presence of <scene name='Sandbox_48/Chain_a__w__waterligand/1'>solvent</scene>, the polar, hydrophilic residues of adenylate kinase interact with the molecules of solvent (purple). There is also solvent accessibility near the center of the molecule at the active site, and it is also accessible on the outward chains like the alpha helices. The ligand (green) is highlighted to show that the water molecules surround the ligand in the middle of the ligand, but not by the ends. | ||
| + | |||
| + | == Ligand Interaction == | ||
| + | |||
| + | There are charged residues that <scene name='Sandbox_48/Ligand__interaction__charges/1'>interact with the ligand</scene>, or make up the interaction site. The positively charged (blue) residues of the enzyme, which would include arginine (R123, R156, R167) and lysine (K13) interact with the negatively charged (red) residues of the ligand. There are also negatively charged portions of the active site, such as aspartic acid (D158, D159) that will interact with positively charged residues of the ligand. | ||
| + | |||
| + | The <scene name='Sandbox_48/Adenylate_kinase_ligand/1'>ligand</scene> pictured is the inhibitory, non-hydrolyzable version of a substrate. It is similar in structure to ATP, but at the end of the triphosphate there is another adenosine. This will stop the reaction, and will allow our enzyme's structure to be analyzed in presence of a substrate. | ||
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 |
Adenylate Kinase
(or ADK) is an enzyme known to catalyze the reversible interconversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to two molecules of adenosine diphosphate (ADP).
Reaction Scheme: ATP + AMP ⇔ 2 ADP
This enzyme is important for cellular energy homeostasis because the need for ADP. ADP is required for oxidative phosphorylation, an important step in multiple metabolic pathways.
Secondary Structure & Hydrogen Bonds
The structure of demonstrates the types of secondary structure that make up the enzyme.
The of chain A of adenylate kinase includes alpha- (green), and (blue). There are 12 total helices in the enzyme, and 2 types of beta sheets, a parallel with 5 strands and an antiparallel with 2 strands. The location of the (black) within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded.
Hydrophobic and Hydrophilic Residues
Within these structures the residues (purple) are located closest on the inside of the enzyme. The residues (green), which are those that are charged or polar, are on the outward face of the enzyme.
Solvent Accessibility
In the presence of , the polar, hydrophilic residues of adenylate kinase interact with the molecules of solvent (purple). There is also solvent accessibility near the center of the molecule at the active site, and it is also accessible on the outward chains like the alpha helices. The ligand (green) is highlighted to show that the water molecules surround the ligand in the middle of the ligand, but not by the ends.
Ligand Interaction
There are charged residues that , or make up the interaction site. The positively charged (blue) residues of the enzyme, which would include arginine (R123, R156, R167) and lysine (K13) interact with the negatively charged (red) residues of the ligand. There are also negatively charged portions of the active site, such as aspartic acid (D158, D159) that will interact with positively charged residues of the ligand.
The pictured is the inhibitory, non-hydrolyzable version of a substrate. It is similar in structure to ATP, but at the end of the triphosphate there is another adenosine. This will stop the reaction, and will allow our enzyme's structure to be analyzed in presence of a substrate.
