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| | <!-- PLEASE DO NOT DELETE THIS TEMPLATE --> | | <!-- PLEASE DO NOT DELETE THIS TEMPLATE --> |
| | {{Template:Oberholser_Sandbox_Reservation}} | | {{Template:Oberholser_Sandbox_Reservation}} |
| - | == '''Introduction''' == | + | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> |
| - | Pancreatic lipase (EC 3.1.1.3) is an esterase enzyme secreted from the pancreas. It breaks down lipids in the digestive system by ester hydrolysis. It converts its triglyceride substrates to monoglycerides and free acids by ester hydrolysis. <ref>"Pancreatic lipase". Wikipedia: The Free Encyclopedia. 7 Nov 2011 [http://en.wikipedia.org/wiki/Pancreatic_lipase]</ref> Pancreatic triglyceride lipase is critical for the efficient absorption of dietary fats.<ref>"Colipase". Wikipedia: The Free Encyclopedia. 5 July 2011 [http://en.wikipedia.org/wiki/Colipase]</ref>
| + | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Act IV Scene iii' /> |
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| - | <StructureSection load='1hpl' size='500' frame='true' align='right' scene='Sandbox_47/Liipase/1' caption='Lipase shown at 2.3 Angstrom resolution' />
| + | ==Introduction== |
| | + | Adenylate kinase has homologs in many species and is an enzyme that converts one ATP and one AMP into two ADP molecules. For simplicity this page will focus on the form found in the bacterium ''Yersinia pestis''. It usually functions with two identical subunits, <scene name='Sandbox_47/Adenylate_kinase_chain_a/1'>Chain A</scene> and chain B, but for simplicity it is easier to focus on one chain. |
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| - | == '''Structure''' == | + | ==Structural Elements== |
| - | Horse pancreatic lipase (PDB ID-1HPL) is an asymmetrical molecule that consists of two subunits, each of which contains 449 amino acids. The two subunits, <scene name='Sandbox_47/Chain_a/3'>A</scene> and
| + | Adenylate kinase has multiple units of <scene name='Sandbox_47/Adenylate_kinase_secondary/1'>Secondary Structure</scene>, including alpha helices (blue) and beta sheets (red). The protein structure is held together with <scene name='Sandbox_47/Ade_kin__secondary_hbond/1'>hydrogen bonds</scene> (green, not working). Looking at the hydrogen bonds demonstrates that the sheets are parallel in conformation, because the hydrogen bonds form trapezoids. |
| - | <scene name='Sandbox_47/B/1'>B</scene>, interact through a variety of <scene name='Sandbox_47/Lipasecontacts/1'>contacts</scene>. The subunits are related by a 2-fold non-crystallographic symmetry axis. Lipase also binds two <scene name='Sandbox_47/Lipase_calcium/2'>calcium ions</scene> as ligands with asparagine, glutamine, and arginine <scene name='Sandbox_47/ conta/4'>contacts</scene>. Calcium promotes the folding of lipase into its active dimer state and holds it in the active state during fat hydrolysis. Its <scene name='Sandbox_47/Lipasesecondarystructures/1'>secondary structure</scene> consists of 22% <scene name='Sandbox_47/Lipase_helix/2'>helices</scene> and 30% <scene name='Sandbox_47/Lipase_sheet/2'>beta sheets</scene>. It contains both <scene name='Sandbox_47/Lipase_hydrophobicres/2'>hydrophobic</scene> (red) and <scene name='Sandbox_47/Lipase_polarres/1'>polar residues</scene> (blue). The overall molecular structure of horse lipase has two well-defined domains. The <scene name='Sandbox_47/Nterminal/1'>N-terminal</scene> domain (residues 1-336) contains the
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| - | <scene name='Sandbox_47/Active/1'>active site</scene> and has a typical alpha/beta hydrolase fold topology. The active site contains a catalytic triad (Ser-152, Asp-176, and His-263) that closely resembles that of serine proteases. The N-terminal domain also contains a <scene name='Sandbox_47/Lid/1'>"lid"</scene> that blocks solvent from entering the active site. The <scene name='Sandbox_47/Cterminal/1'>C-terminal</scene> domain (residues (337-449), for colipase binding, has a beta-sheet sandwich topology.<ref>Bourne Y, Martinez C, Kerfelec B, Lombardo D, Chapus C, Cambillau C. 1994. Horse pancreatic lipase. J. mol Biol. 238: 709-732.</ref>
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| | + | The <scene name='Sandbox_47/Ad_k_hydrophobic/3'>Hydrophobic Residues</scene> (gray) of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the <scene name='Sandbox_47/Adenylate_kinase_hydrophillic/1'>polar residues</scene> (orange) are either on the exterior surface, where they can be accessed by the solvent, or in close interaction with each other. Some polar residues also center around the entrance to the active site, to aid the desolvation of the ligand. A combined view of both the <scene name='Sandbox_47/Ad_k_hydrophillic_and_phobic/1'>Hydrophillic and Hydrophobic Residues</scene> allows one to see the general patterns of arrangement relative to each other. |
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| - | <embed type=”application/x-shockwave-flash” flashvars=”audioUrl=MP3_FILE_URL” src=”http://www.google.com/reader/ui/3523697345-audio-player.swf” width=”400″ height=”27″ quality=”best”></embed> | + | The hydrophillic residues often find themselves in interactions with the <scene name='Sandbox_47/Adenylate_kinase_water/1'>water</scene> |
| | + | (purple) that is solvating the enzyme. Water surrounds the outer surface of the protein, which is to be expected, but it is also possible to see that water molecules have interactions in some of the deeper parts of the protein as well, especially near the active site. |
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| - | == '''Function''' ==
| + | Of course, the areas of the protein that interact with the substrates are the most interesting parts, so the <scene name='Sandbox_47/Ad_k_ligand_interaction/1'>ligand stabilizing residues</scene> (red) are important to note. The residues of the active site are the most critical parts of the protein, because they actually do the chemical reactions of the enzyme. The <scene name='Sandbox_47/Ad_k_active_site/1'>active site</scene> residues (purple) are shown here. |
| - | Most lipases act at a specific position on the glycerol backbone of the lipid substrate.<ref>"Lipase". Wikipedia: The Free Encyclopedia. 6 Nov 2011 [http://en.wikipedia.org/wiki/Lipase]</ref> Pancreatic lipase catalyzes the hydrolysis of triacylglycerols at their 1 and 3 positions to form 1,2-diacylglycerols and 2-acylglycerols together with the Na+ and K+ salts of fatty acids. The enzymatic activity of pancreatic lipase increases when it contacts the lipid-water interface. Binding to the lipid-water interface requries mixed micelles of phosphatidylcholine and bile acids as well as colipase.<ref>Voet D, Voet JG, Pratt CW. "Fundamentals of Biochemistry: Life at the Molecular Level" John Wiley and Sons, Inc: New Jersey, 2008..</ref>
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| - | [[Image:Hydrolysis.gif|200px|right|thumb| Lipase-catalyzed hydrolysis of lipids. Notice the catalytic triad of Ser-152, Asp-176, and His-263 that constitute the active site.<ref>http://www.pnas.org/content/101/16/5716.full</ref>]]
| + | ==Sources== |
| | + | http://www.proteopedia.org/wiki/index.php/Adenylate_kinase |
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| - | == '''Colipase''' == | + | ==Scenes== |
| - | Unlike many proteases, pancreatic lipase is secreted in its final form. However, it is only active in the presence of <scene name='Sandbox_47/Colipase/2'>colipase</scene>in the duodenum. Colipase is a 90-residue protein that forms a 1:1 <scene name='Sandbox_47/Colipasecontacts/2'>complex with lipase</scene>.<ref>Voet D, Voet JG, Pratt CW. "Fundamentals of Biochemistry: Life at the Molecular Level" John Wiley and Sons, Inc: New Jersey, 2008..</ref><ref>"van Tilbeurgh H, Sarda L, Verger R, Cambillau C. 1992. Structure of the pancreatic lipase-procolipase complex. Nature 359: 159-162. </ref> Colipase is also secreted in the pancreas, but in its inactive form, procolipase, which is activated by trypsin in the intestinal lumen. Colipase prevents the inhibitory effect of bile salts on the lipase-catalyzed intraduodenal hydrolysis of dietary long-chain triglycerides. Colipase binds to the <scene name='Sandbox_47/C-termina/1'>C-terminal</scene>, non-catalytic domain of lipase, which stabilizes the active conformation and increases the hydrophobicity of the binding site.<ref>"Colipase". Wikipedia: The Free Encyclopedia. 5 July 2011 [http://en.wikipedia.org/wiki/Colipase]</ref> In other words, colipase activates the enzyme through the movement of the N-terminal domain loop or lid. Here, lipase and colipase can be seen <scene name='Sandbox_47/Lipasecolipasesubstrate/1'>in complex with a triacylglycerol</scene>.<ref>Hermoso J, Pignol D, Kerfelec B, Crenon I, Chapus C, Fontecilla-Camps JC. 1996. Lipase activation by nonionic detergents. J. Biol. Chem. 271: 18007-18016.</ref>
| + | (Just for reference) |
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| - | == '''Mechanism''' ==
| + | <scene name='Sandbox_47/Adenylate_kinase_chain_a/1'>Chain A</scene> |
| - | The mechanism of pancreatic lipase begins with His263 deprotonating Ser152, which attacks the carboxy carbon of the triacylglycerol substrate in a nucleophilic addition. In the second step, the oxyanion collapses, initiating an elimination of the diacylglycerol product, which deprotonates His263 and acylated Ser152. Next, His263 deprotonates water, which attacks the carboxyl carbon of the acylated Ser152 in a nucleophilic addition. Finally, the oxyanion collapses, initiating an elimination of the carboxylate product, and Ser152, which deprotonates His263.<ref>"Overview for MACiE Entry M0218". EMBL-EBI. 17 June 2008. [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=M0218]</ref>
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| - | == '''Inhibition''' ==
| + | <scene name='Sandbox_47/Adenylate_kinase_secondary/1'>Secondary Structure</scene> |
| - | C11 alkyl phosphonate is an effective inhibitor of pancreatic lipase. The binding of the ligand induces rearrangements of two surface loops in comparison with the closed structure of the enzyme. The inhibitor covalently binds to the active site serine Ser152, as seen in this image of the <scene name='Sandbox_47/Inhibitor/1'>lipase colipase complex inhibited by C11 alkyl phosphate</scene>. Evidence exists that the active site binds both of the enantiomers of C11 phosphonate. The C11 alkyl chain of the first enantiomer fits into a hydrophobic groove and is thought to mimic the interaction between the leaving fatty acid of a triglyceride substrate and the protein. The alkyl chain of the second enantiomer also has an elongated conformation and interacts with hydrophobic patches on the surface of the open amphipathic lid. This may indicate the location of a second alkyl chain of a triglyceride substrate.<ref>Egloff MP, Marguet F, Buono G, Verger R, Cambillau C, van Tilbeurgh H. 1995. The 2.46 A resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 phosphonate. Biochemistry 34: 2751-2762.</ref>
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| - | == '''Clinical Significance''' ==
| + | <scene name='Sandbox_47/Ade_kin__secondary_hbond/1'>hydrogen bonds</scene> |
| - | Pancreatic lipase is secreted into the duodenum through the duct system of the pancreas. In a healthy individual, it is in very low concentration in serum. Under extreme disruption of pancreatic function, such as pancreatitis or pancreatic cancer, the pancreas may begin to digest itself and release pancreatic enzymes including pancreatic lipase into serum. Measurement of serum concentration of pancreatic lipase can therefore aid in diagnosis of acute pancreatitis.<ref>"Pancreatic lipase". Wikipedia: The Free Encyclopedia. 7 Nov 2011 [http://en.wikipedia.org/wiki/Pancreatic_lipase]</ref>
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| - | == '''References''' == | + | <scene name='Sandbox_47/Ad_k_hydrophobic/3'>Hydrophobic Residues</scene> |
| - | <references /> | + | |
| | + | <scene name='Sandbox_47/Adenylate_kinase_hydrophillic/1'>Polar Residues</scene> |
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| | + | <scene name='Sandbox_47/Ad_k_hydrophillic_and_phobic/1'>Hydrophillic and Hydrophobic Residues</scene> |
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| | + | <scene name='Sandbox_47/Adenylate_kinase_water/1'>Water</scene> |
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| | + | <scene name='Sandbox_47/Ad_k_ligand_interaction/1'>ligand stabilizing residues</scene> |
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| | + | <scene name='Sandbox_47/Ad_k_active_site/1'>active site</scene> |
Adenylate kinase has homologs in many species and is an enzyme that converts one ATP and one AMP into two ADP molecules. For simplicity this page will focus on the form found in the bacterium Yersinia pestis. It usually functions with two identical subunits, and chain B, but for simplicity it is easier to focus on one chain.
Adenylate kinase has multiple units of , including alpha helices (blue) and beta sheets (red). The protein structure is held together with (green, not working). Looking at the hydrogen bonds demonstrates that the sheets are parallel in conformation, because the hydrogen bonds form trapezoids.
The (gray) of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the (orange) are either on the exterior surface, where they can be accessed by the solvent, or in close interaction with each other. Some polar residues also center around the entrance to the active site, to aid the desolvation of the ligand. A combined view of both the allows one to see the general patterns of arrangement relative to each other.
The hydrophillic residues often find themselves in interactions with the
(purple) that is solvating the enzyme. Water surrounds the outer surface of the protein, which is to be expected, but it is also possible to see that water molecules have interactions in some of the deeper parts of the protein as well, especially near the active site.
Of course, the areas of the protein that interact with the substrates are the most interesting parts, so the (red) are important to note. The residues of the active site are the most critical parts of the protein, because they actually do the chemical reactions of the enzyme. The residues (purple) are shown here.
