Sandbox 44
From Proteopedia
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</p>Weight: 50kDa<p></p> | </p>Weight: 50kDa<p></p> | ||
==Introduction== | ==Introduction== | ||
| - | The lipase class of enzymes are known to cut a lipid substrate at a specific location on their glycerol backbone. Lipase catalyzes the lipid breakdown through the hydrolysis of the esters in fatty acids.<ref>1HPL PDB SUM</ref> While lipase is found primarily in the human pancreas, lipase can also be located in other areas in the body such as the mouth and the stomach. Pancreatic lipase, in particular, serves in human digestion to break down fats from the human diet. This lipase, therefore, is found in the digestive system of humans and is involved in the conversion of triglycerides to monoglycerides and free fatty acids. It is made by the pancreas and secreted into the duodenum, in which it will serve to break down fats.<ref>Voet, D., et al. "Fundamentals of biochemistry: life at the molecular level." John Wiley & Sons, Inc. Hoboken, 2008.</ref><p> | + | The lipase class of enzymes are known to cut a lipid substrate at a specific location on their glycerol backbone. Lipase catalyzes the lipid breakdown through the hydrolysis of the esters in fatty acids.<ref>1HPL PDB SUM [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1hpl&template=main.html]</ref> While lipase is found primarily in the human pancreas, lipase can also be located in other areas in the body such as the mouth and the stomach. Pancreatic lipase, in particular, serves in human digestion to break down fats from the human diet. This lipase, therefore, is found in the digestive system of humans and is involved in the conversion of triglycerides to monoglycerides and free fatty acids. It is made by the pancreas and secreted into the duodenum, in which it will serve to break down fats.<ref>Voet, D., et al. "Fundamentals of biochemistry: life at the molecular level." John Wiley & Sons, Inc. Hoboken, 2008.</ref><p> |
| - | Human pancreatic lipase distinguishes itself from other pancreatic enzymes because when it is synthesized it is done so in its final form, without needing to be activated through proteolytic cleavage.<ref>"Pancreatic lipase." Wikipedia: the free encylopedia, 7 Nov 2011 </ref> However, while lipase does not need outside activation, it is not truly efficient without the presence of colipase in the duodenum.</p><p> | + | Human pancreatic lipase distinguishes itself from other pancreatic enzymes because when it is synthesized it is done so in its final form, without needing to be activated through proteolytic cleavage.<ref>"Pancreatic lipase." Wikipedia: the free encylopedia, 7 Nov 2011 [http://en.wikipedia.org/wiki/Human_pancreatic_lipase]</ref> However, while lipase does not need outside activation, it is not truly efficient without the presence of colipase in the duodenum.</p><p> |
| - | The crystal structure of human pancreatic lipase is still yet to be determined and the research goal of many current scientists. Therefore, the structure examined here, 1HPL, is in actuality horse pancreatic lipase, thought to have a very similar structure as well as function with regard to human pancreatic lipase.<ref>Bourne, Y., et al. ""Horse pancreatic lipase. The crystal structure defined at 2.3 A resolution"(1994) J.Mol.Biol. 238: 709-732</ref> | + | The crystal structure of human pancreatic lipase is still yet to be determined and the research goal of many current scientists. Therefore, the structure examined here, 1HPL, is in actuality horse pancreatic lipase, thought to have a very similar structure as well as function with regard to human pancreatic lipase.<ref>Bourne, Y., et al. ""Horse pancreatic lipase. The crystal structure defined at 2.3 A resolution"(1994) J.Mol.Biol. 238: 709-732 [http://www.pdb.org/pdb/explore/explore.do?structureId=1HPL]</ref> |
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<StructureSection load='1hpl' size='500' side='right' caption='Lipase (PDB entry [[1hpl]])' scene=''> | <StructureSection load='1hpl' size='500' side='right' caption='Lipase (PDB entry [[1hpl]])' scene=''> | ||
The <scene name='Sandbox_44/Structure_of_lipase/1'>structure of lipase</scene> displays the enzyme in its natural form, with its two identical chains, each consisting of 449 amino acid residues.<ref>Bourne, Y., et al. "Horse pancreatic lipase..."</ref> The <scene name='Sandbox_44/Secondary_structure/3'>secondary structures</scene> of human pancreatic lipase consists of 30% beta sheets (shown in orange), and 22% alpha helices (shown in fuschia).<ref>Bourne, Y., et al. "Horse pancreatic lipase..."</ref> Here, beta sheets are depicted as planks, and alpha helices are shown as rockets. The remaining 48% of the enzyme's secondary structure consists of ordered, nonrepetitive sequence structure (shown in white) in contrast to the alpha helices and beta sheets. This even distribution of 48% ordered nonrepetitive structure to 52% alpha helix/beta sheet structure correlates to the appearance of the structure of lipase, which appears even to the casual observer to be about half alpha helix/beta sheet structure, and half ordered nonrepetitive structure depicted through the looping connective lines. This secondary structure of the enzyme, however, is formed due to the nature of the hydrogen bonding in between the main chains of lipase. These <scene name='Sandbox_44/Hydrogen_bonding/1'>hydrogen bonds</scene> can be seen throughout the structure of lipase, displayed here in bright yellow for clarity. <p> | The <scene name='Sandbox_44/Structure_of_lipase/1'>structure of lipase</scene> displays the enzyme in its natural form, with its two identical chains, each consisting of 449 amino acid residues.<ref>Bourne, Y., et al. "Horse pancreatic lipase..."</ref> The <scene name='Sandbox_44/Secondary_structure/3'>secondary structures</scene> of human pancreatic lipase consists of 30% beta sheets (shown in orange), and 22% alpha helices (shown in fuschia).<ref>Bourne, Y., et al. "Horse pancreatic lipase..."</ref> Here, beta sheets are depicted as planks, and alpha helices are shown as rockets. The remaining 48% of the enzyme's secondary structure consists of ordered, nonrepetitive sequence structure (shown in white) in contrast to the alpha helices and beta sheets. This even distribution of 48% ordered nonrepetitive structure to 52% alpha helix/beta sheet structure correlates to the appearance of the structure of lipase, which appears even to the casual observer to be about half alpha helix/beta sheet structure, and half ordered nonrepetitive structure depicted through the looping connective lines. This secondary structure of the enzyme, however, is formed due to the nature of the hydrogen bonding in between the main chains of lipase. These <scene name='Sandbox_44/Hydrogen_bonding/1'>hydrogen bonds</scene> can be seen throughout the structure of lipase, displayed here in bright yellow for clarity. <p> | ||
| - | There are two main chains in human pancreatic lipase, shown here as Chain A and Chain B. <scene name='Sandbox_44/Chain_a/1'>Chain A</scene> (in blue) is exactly identical to <scene name='Sandbox_44/Chain_b/1'>Chain B</scene> (in green), and each chain has two domains which can be identified through <scene name='Sandbox_44/N-c_rainbow/1'>N terminus to C terminus labeling</scene>. This rainbow labeling displays the N-terminus domain of each chain in blue, leading in a color spectrum fashion to the C-terminus domain of each chain in red. These two sections of each chain are not identical in composition, however, as the N-terminus 337 residues long, comprised mainly in a 3 layer sandwich known as alpha, beta, alpha sandwich. The C-terminus, in comparison, contains a mere 112 residues that are ordered primarily in beta sandwich fashion.<ref>1HPL PDB SUM</ref> The C-terminus of lipase is where its enzyme colipase binds.</p><ref>van Tilbeurgh H, etc."Structure of the pancreatic lipase-procolipase complex", 1992 Sep 10;359(6391):159-62. PMID:1522902</ref> | + | There are two main chains in human pancreatic lipase, shown here as Chain A and Chain B. <scene name='Sandbox_44/Chain_a/1'>Chain A</scene> (in blue) is exactly identical to <scene name='Sandbox_44/Chain_b/1'>Chain B</scene> (in green), and each chain has two domains which can be identified through <scene name='Sandbox_44/N-c_rainbow/1'>N terminus to C terminus labeling</scene>. This rainbow labeling displays the N-terminus domain of each chain in blue, leading in a color spectrum fashion to the C-terminus domain of each chain in red. These two sections of each chain are not identical in composition, however, as the N-terminus 337 residues long, comprised mainly in a 3 layer sandwich known as alpha, beta, alpha sandwich. The C-terminus, in comparison, contains a mere 112 residues that are ordered primarily in beta sandwich fashion.<ref>1HPL PDB SUM</ref> The C-terminus of lipase is where its enzyme colipase binds.</p><ref>van Tilbeurgh H, etc."Structure of the pancreatic lipase-procolipase complex", 1992 Sep 10;359(6391):159-62. PMID:1522902 [http://www.proteopedia.org/wiki/index.php/1n8s]</ref> |
<p>The <scene name='Sandbox_44/Active_site_chain_a/1'>active site of Chain A</scene> is seen here highlighted in yellow, located within the N-terminus in residues 1-336. This active site contains a catalytic triad of Ser 152, His 263, and Asp 176 that facilitate the ester hydrolysis reaction carried out by lipase. This catalytic triad is very similar to that in a serine protease enzyme.<ref> Voet, D., et al. "Fundamentals of biochemistry"</ref> However, if no lipid micelles are present for digestion, the active site of lipase (containing this catalytic triad of Ser, His, and Asp) is covered with a "lid" composed of 25 residues in a helical fashion.</p><ref> Voet, D., et al. "Fundamentals of biochemistry</ref> | <p>The <scene name='Sandbox_44/Active_site_chain_a/1'>active site of Chain A</scene> is seen here highlighted in yellow, located within the N-terminus in residues 1-336. This active site contains a catalytic triad of Ser 152, His 263, and Asp 176 that facilitate the ester hydrolysis reaction carried out by lipase. This catalytic triad is very similar to that in a serine protease enzyme.<ref> Voet, D., et al. "Fundamentals of biochemistry"</ref> However, if no lipid micelles are present for digestion, the active site of lipase (containing this catalytic triad of Ser, His, and Asp) is covered with a "lid" composed of 25 residues in a helical fashion.</p><ref> Voet, D., et al. "Fundamentals of biochemistry</ref> | ||
<p>The identical <scene name='Sandbox_44/Active_site_2/1'>active site of Chain B</scene> is shown here in red, also facilitating the reaction, the mechanism of which will be discussed below. | <p>The identical <scene name='Sandbox_44/Active_site_2/1'>active site of Chain B</scene> is shown here in red, also facilitating the reaction, the mechanism of which will be discussed below. | ||
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The activity of bile salts as described above are simply not enough for pancreatic lipase to function properly and efficiently; rather, lipase requires the aid of its coenzyme colipase<ref>van Tilbeurgh, H., et al. "Structure of the pancreatic lipase procolipase complex"</ref>, which binds to the <scene name='Sandbox_44/C_terminal_contact/1'>C-terminal domain of lipase</scene>(residues 337-449). This binding of colipase to lipase occurs opposite of the active site on the C-terminal, and contacts between them include Van der Waals forces and other polar interactions like salt bridges in order to achieve maximum stability between enzyme and coenzyme.<p> | The activity of bile salts as described above are simply not enough for pancreatic lipase to function properly and efficiently; rather, lipase requires the aid of its coenzyme colipase<ref>van Tilbeurgh, H., et al. "Structure of the pancreatic lipase procolipase complex"</ref>, which binds to the <scene name='Sandbox_44/C_terminal_contact/1'>C-terminal domain of lipase</scene>(residues 337-449). This binding of colipase to lipase occurs opposite of the active site on the C-terminal, and contacts between them include Van der Waals forces and other polar interactions like salt bridges in order to achieve maximum stability between enzyme and coenzyme.<p> | ||
When colipase binds to the nonactive site of the C-terminal domain of lipase, then, the lipase enzyme is stabilized enough so that it may proceed with any hydrophobic interactions between itself and the triacylglycerides. This binding of colipase essentially activates lipase so that it can effectively break down fats in the body; the association of colipase and lipase is what makes lipase a true catalyst.</p> | When colipase binds to the nonactive site of the C-terminal domain of lipase, then, the lipase enzyme is stabilized enough so that it may proceed with any hydrophobic interactions between itself and the triacylglycerides. This binding of colipase essentially activates lipase so that it can effectively break down fats in the body; the association of colipase and lipase is what makes lipase a true catalyst.</p> | ||
| - | <p>When lipid micelles are present, the 25-residue "lid" over the active site undergoes a conformational changes in order that the active site may be exposed. At the same time, the beta 5 loop (consisting of 10 residues) also undergoes a conformational change to make an oxyanion hole for the enzyme, thereby creating a hydrophobic surface close to the active site entryway. This beta 5 loop had previously (before the coenzyme's binding) served to protect the oxyanion hole, but now it can reveal the hole for the reaction to proceed.<ref>Lennens, M. & Lowe, Mark. "A surface loop covering the active site of human pancreatic lipase influences interfacial activation and lipid binding." 14 Oct, 1994 The Journal of Biological Chemistry, 269, 25470-25474.</ref> As colipase binds, it forms three additional hydrogen bonds to the recently opened "lid" of the active site so as to most effectively stabilize the lid in its open position.<ref>Eydoux, C., et al. "Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation." 15 Aug, 2008. DOI: 10.1021/bi8005576 </ref> After the binding of colipase, lipase completes a hydrolysis very similar to that of a serine protease through the use of its catalytic triad. This hydrolysis eventually releases the desired broken-down lipid products.</p> | + | <p>When lipid micelles are present, the 25-residue "lid" over the active site undergoes a conformational changes in order that the active site may be exposed. At the same time, the beta 5 loop (consisting of 10 residues) also undergoes a conformational change to make an oxyanion hole for the enzyme, thereby creating a hydrophobic surface close to the active site entryway. This beta 5 loop had previously (before the coenzyme's binding) served to protect the oxyanion hole, but now it can reveal the hole for the reaction to proceed.<ref>Lennens, M. & Lowe, Mark. "A surface loop covering the active site of human pancreatic lipase influences interfacial activation and lipid binding." 14 Oct, 1994 The Journal of Biological Chemistry, 269, 25470-25474. [http://www.jbc.org/content/269/41/25470.full.pdf+html]</ref> As colipase binds, it forms three additional hydrogen bonds to the recently opened "lid" of the active site so as to most effectively stabilize the lid in its open position.<ref>Eydoux, C., et al. "Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation." 15 Aug, 2008. DOI: 10.1021/bi8005576 [http://pubs.acs.org/doi/abs/10.1021/bi8005576]</ref> After the binding of colipase, lipase completes a hydrolysis very similar to that of a serine protease through the use of its catalytic triad. This hydrolysis eventually releases the desired broken-down lipid products.</p> |
<p>Chemically, the mechanism of triacylglycerol by lipase is achieved only through the reactions of the His, Ser, and Asp residues of the active site, as well as with aid from the stabilizing effects of nearby Phe 77 and Leu 153 found in the oxyanion hole. | <p>Chemically, the mechanism of triacylglycerol by lipase is achieved only through the reactions of the His, Ser, and Asp residues of the active site, as well as with aid from the stabilizing effects of nearby Phe 77 and Leu 153 found in the oxyanion hole. | ||
Revision as of 05:35, 14 November 2011
| 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. |
Contents |
Lipase
PDB ID: 1HPLE.C.: 3.1.1.3
Number of Amino Acid Residues: 449
Number of Chains: 2
Weight: 50kDa
Introduction
The lipase class of enzymes are known to cut a lipid substrate at a specific location on their glycerol backbone. Lipase catalyzes the lipid breakdown through the hydrolysis of the esters in fatty acids.[1] While lipase is found primarily in the human pancreas, lipase can also be located in other areas in the body such as the mouth and the stomach. Pancreatic lipase, in particular, serves in human digestion to break down fats from the human diet. This lipase, therefore, is found in the digestive system of humans and is involved in the conversion of triglycerides to monoglycerides and free fatty acids. It is made by the pancreas and secreted into the duodenum, in which it will serve to break down fats.[2]Human pancreatic lipase distinguishes itself from other pancreatic enzymes because when it is synthesized it is done so in its final form, without needing to be activated through proteolytic cleavage.[3] However, while lipase does not need outside activation, it is not truly efficient without the presence of colipase in the duodenum.
The crystal structure of human pancreatic lipase is still yet to be determined and the research goal of many current scientists. Therefore, the structure examined here, 1HPL, is in actuality horse pancreatic lipase, thought to have a very similar structure as well as function with regard to human pancreatic lipase.[4]
Structural Aspects of Lipase
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Function of Lipase
As mentioned above, lipase serves to catalyze the hydrolysis of triacylglycerols into 2-monoacylglyercols and fatty acids.[12] This breakdown of triacylglycerols in digestion is an enormous means of energy storage, and is extremely useful in human metabolism as fats from our diet are broken down.Lipase must be at the precise orientation in order to digest fats; this requires several factors to be in order for proper triacylglycerol breakdown. First, the calcium ion ligand must be present; second, the coenzyme of lipase (colipase) must be present and in the proper orientation; and finally, bile salts must be at the ready to aid in the process of breaking down fats.
The triacylglycerols in their initial form are not soluble in water, yet pancreatic lipase is very much water soluble, and therefore will digest these triacylglycerols at lipid-water interfaces where both are content, so to speak. How fast this digestion of triacylglycerols occurs depends largely on the size of the lipid-water interface; they are indirectly proportional to each other. Bile salts facilitate increased rates of triacylglycerol digestion in the intestine as they emulsify and solubilize fat globules. These bile salts, then, surround the globules of fatty acids and work to make them more soluble for breakdown.[13]
Mechanism of Lipase
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References
- ↑ 1HPL PDB SUM [1]
- ↑ Voet, D., et al. "Fundamentals of biochemistry: life at the molecular level." John Wiley & Sons, Inc. Hoboken, 2008.
- ↑ "Pancreatic lipase." Wikipedia: the free encylopedia, 7 Nov 2011 [2]
- ↑ Bourne, Y., et al. ""Horse pancreatic lipase. The crystal structure defined at 2.3 A resolution"(1994) J.Mol.Biol. 238: 709-732 [3]
- ↑ Bourne, Y., et al. "Horse pancreatic lipase..."
- ↑ Bourne, Y., et al. "Horse pancreatic lipase..."
- ↑ 1HPL PDB SUM
- ↑ van Tilbeurgh H, etc."Structure of the pancreatic lipase-procolipase complex", 1992 Sep 10;359(6391):159-62. PMID:1522902 [4]
- ↑ Voet, D., et al. "Fundamentals of biochemistry"
- ↑ Voet, D., et al. "Fundamentals of biochemistry
- ↑ Voet, D., et al. "Fundamentals of biochemistry"
- ↑ 1HPL PDB SUM
- ↑ Voet, D., et al. "Fundamentals of biochemistry"
- ↑ van Tilbeurgh, H., et al. "Structure of the pancreatic lipase procolipase complex"
- ↑ Lennens, M. & Lowe, Mark. "A surface loop covering the active site of human pancreatic lipase influences interfacial activation and lipid binding." 14 Oct, 1994 The Journal of Biological Chemistry, 269, 25470-25474. [5]
- ↑ Eydoux, C., et al. "Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation." 15 Aug, 2008. DOI: 10.1021/bi8005576 [6]
