Sandbox Reserved 914

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This Sandbox is Reserved from Jan 06, 2014, through Aug 22, 2014 for use by the Biochemistry II class at the Butler University at Indianapolis, IN USA taught by R. Jeremy Johnson. This reservation includes Sandbox Reserved 911 through Sandbox Reserved 922.

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Palmitoyl-Protein Thioesterase 1

Three dimensional structure of Palmitoyl-Protein Thioesterase 1.

Palmitoyl-Protein Thioesterase 1 (PPT1) is a lysosomal enzyme that plays a role in the degradation of lipid-modified proteins^[1]. PPT1 receives its catalytic power from its catalytic triad, the α/β hydrolase fold, and its hydrophobic groove in order to remove fatty acid acyl groups, typically palmitate from cysteine residues in proteins. PPT1 demonstrates how proteins can be modified by different enzymes and induce biological changes ^[1]. Misregulation of PPT1 modifications can cause various diseases, including infantile neuronal ceroid lipofuscinosis, kufs disease, and late-infantile neuronal ceroid lipofuscinosis. Within these diseases, the production of PPT1 is decreased or eliminated completely, which leads to fatty acid buildup ^[2].

1 Structure
2 Function
- 2.1 Biological
- 2.2 Molecular
3 Medical Relevance

Structure

The secondary structure of PPT1 contains several α-helices and few β-sheets. PPT1 includes residues 28-306, after the 27-residue signal peptide has been removed ^[3]. There is a large insertion between β6 and β7, residues 140-223, and that forms a second domain that is compromised almost entirely of the fatty acid binding site. This second domain region contains six helices, α2-α7^[3].

α/β Hydrolase Fold

The α/β Hydrolase Fold is common to many other hydrolases. The α/β hydrolase fold has a central 6 stranded parallel β-sheet consisting of and α-helices ^[3]. It also consists of a catalytic triad and an oxyanion hole. The pKa of the nucleophile in the catalytic triad is lowered to allow the nucleophilic attack^[4]. None of the enzymes within the α/β hydrolase fold family require a cofactor for catalytic activity.

Catalytic Triad

The is composed of Ser115, His289, and Asp233, which is the same as the catalytic triad in chymotrypsin. A water molecule is occupying the and it is hydrogen bonded to Ser115 ^[4]. The purpose of the oxyanion hole is to stabilize the oxyanion that is formed after the nucleophilic attack, which happens to be in the transition state. Ser115 acts as a nucleophile, while His289 and Asp233 are coordinated to Ser115 to lower its pKa value so it can undergo catalytic activity^[4].

Hydrophobic Groove

The is located in the second domain of PPT1, where palmitate mainly binds. The fact that palmitate has to to fit into the binding pocket suggests that this pocket is designed to bind an unsaturated fatty acid, with a possible cis-double bond between C4 and C5^[3]. The top portion of the groove is formed by the residues from α2 to α3. Several residues that are present near the active site create the rest of the groove, including Ile235, Val236, Gln116, Gly40, and Met41^[3].

Function

Biological

PPT1 is biologically involved in sensory transduction and the vision process^[5]. Within sensory tranduction, PPT1 is involved in the process of converting extracellular signals, such aws light, taste, touch, or smell, into electric signals that are then sent throughout the body^[5]. With vision, PPT1 is involved in the process of seeing images and then processing them into information that is then interpreted by the brain^[5].

Molecular

The main molecular function of PPT1 is to breakdown lipid-modified proteins and act as a hydrolase of disulfide bonds^[3]. In the main catalytic reaction for PPT1, a cysteine residue is removed from the palmitoylated protein by PPT, resulting in a free cysteine residue and palmitoyl-CoA^[3]. It is suggested that a water molecule comes in and stabilizes the transition state, along with protonating the cysteine residue on the palmitoylated protein, allowing the palmitoyl-CoA to break free.

Medical Relevance

PPT1 mutations are the root cause of several diseases, specifically those where mutations cause a decrease or depletion of PPT1. Infantile neuronal ceroid lipofuscinosis (INCF) is characterized by impaired mental and motor development, including difficulty with walking, speaking, and intellectual function, beginning around the first or second year of life^[2]. The PPT1 mutation involved in INCF replaces an arginine with a stop signal in the instructions to make the enzyme. This mutation leads to a vast reduction in the production of PPT1, which impairs the removal of fatty acids from proteins. This impaired removal leads to fatty acid accumulations throughout the body, particularly in neuronal cells in the brain^[2]. Late-infantile neuronal ceroid lipofuscinosis has the same characteristics as INCF, but the mutation varies slightly. This leads to a slight reduction in the activity of PPT1 instead of completely wiping it out^[2]. Mutations can also cause premature stop signals to be added to the instructions to create PPT1, resulting in Kufs disease^[2]. This is characterized by seizures, problems with movement, and a decline of intellectual function, usually beginning in early adulthood^[2]. Although premature stop signals are added, these mutations allow enough PPT1 to be produced so that the onset is later on in life and the life expectancy is higher.

References

↑ ^1.0 ^1.1 Palmitoyl-Protein Thioesterase 1 Precursor - Homo Sapiens. N.p., 1 Oct. 1996.
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 PPT1. Genetics Home Reference. U.S. National Library of Medicine, Aug. 2015.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 Bellizzi III, John. RCSB Protein Data Bank. PNAS, 18 Apr. 2000.
↑ ^4.0 ^4.1 ^4.2 Branneby, Cecilia. Exploiting Enzyme Promiscuity for Rational Design. KTH Biotechnology. N.p., May 2005
↑ Cite error: Invalid <ref> tag; no text was provided for refs named Human

External Resources

http://en.wikipedia.org/wiki/Palmitoyl_protein_thioesterase

https://www.counsyl.com/diseases/ppt1-related-neuronal-ceroid-lipofuscinosis/

http://en.wikipedia.org/wiki/Alpha/beta_hydrolase_fold

http://en.wikipedia.org/wiki/Catalytic_triad

http://www.biomedcentral.com/1471-2121/8/22

http://www.genecards.org/cgi-bin/carddisp.pl?gene=PPT1

http://www.ebi.ac.uk/pdbe-srv/view/entry/1pja/summary.html

http://www.ncbi.nlm.nih.gov/gene/5538

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_914"

@@ Line 14: / Line 14: @@
 === α/β Hydrolase Fold ===
-The α/β Hydrolase Fold is common to many other hydrolases. The α/β hydrolase fold has a central 6 stranded parallel β-sheet consisting of <scene name='57/573128/4/1'>β3-β8</scene> and α-helices <scene name='57/573128/5/1'>αA, αB, αC, and αF</scene>. It also consists of a catalytic triad and an oxyanion hole. The pKa of the nucleophile in the catalytic triad is lowered to allow the nucleophilic attack. None of the enzymes within the α/β hydrolase fold family require a cofactor for catalytic activity.
+The α/β Hydrolase Fold is common to many other hydrolases. The α/β hydrolase fold has a central 6 stranded parallel β-sheet consisting of <scene name='57/573128/4/1'>β3-β8</scene> and α-helices <scene name='57/573128/5/1'>αA, αB, αC, and αF</scene><ref name="RSCB"/>. It also consists of a catalytic triad and an oxyanion hole. The pKa of the nucleophile in the catalytic triad is lowered to allow the nucleophilic attack<ref name="Prom">Branneby, Cecilia. Exploiting Enzyme Promiscuity for Rational Design. KTH Biotechnology. N.p., May 2005</ref>. None of the enzymes within the α/β hydrolase fold family require a cofactor for catalytic activity.
 === Catalytic Triad ===
 The <scene name='57/573128/2/1'>catalytic triad</scene> is composed of Ser115, His289, and Asp233, which is the same as the catalytic triad in chymotrypsin.
-A water molecule is occupying the <scene name='57/573128/7/1'>oxyanion hole</scene> and it is hydrogen bonded to Ser115. The purpose of the oxyanion hole is to stabilize the oxyanion that is formed after the nucleophilic attack, which happens to be in the transition state. Ser115 acts as a nucleophile, while His289 and Asp233 are coordinated to Ser115 to lower its pKa value so it can undergo catalytic activity.
+A water molecule is occupying the <scene name='57/573128/7/1'>oxyanion hole</scene> and it is hydrogen bonded to Ser115 <ref name="Prom"/>. The purpose of the oxyanion hole is to stabilize the oxyanion that is formed after the nucleophilic attack, which happens to be in the transition state. Ser115 acts as a nucleophile, while His289 and Asp233 are coordinated to Ser115 to lower its pKa value so it can undergo catalytic activity<ref name="Prom"/>.
 ===Hydrophobic Groove ===
-The <scene name='57/573128/3/1'>hydrophobic binding groove</scene> is located in the second domain of PPT1, where palmitate mainly binds. The fact that palmitate has to <scene name='57/573128/6/1'>bend</scene> to fit into the binding pocket suggests that this pocket is designed to bind an unsaturated fatty acid, with a possible cis-double bond between C4 and C5. The top portion of the groove is formed by the residues from α2 to α3. Several residues that are present near the active site create the rest of the groove, including Ile235, Val236, Gln116, Gly40, and Met41.
+The <scene name='57/573128/3/1'>hydrophobic binding groove</scene> is located in the second domain of PPT1, where palmitate mainly binds. The fact that palmitate has to <scene name='57/573128/6/1'>bend</scene> to fit into the binding pocket suggests that this pocket is designed to bind an unsaturated fatty acid, with a possible cis-double bond between C4 and C5<ref name="RSCB"/>. The top portion of the groove is formed by the residues from α2 to α3. Several residues that are present near the active site create the rest of the groove, including Ile235, Val236, Gln116, Gly40, and Met41<ref name="RSCB"/>.
 == Function ==
 ===Biological ===
-PPT1 is biologically involved in sensory transduction and the vision process. Within sensory tranduction, PPT1 is involved in the process of converting extracellular signals, such aws light, taste, touch, or smell, into electric signals that are then sent throughout the body. With vision, PPT1 is involved in the process of seeing images and then processing them into information that is then interpreted by the brain.
+PPT1 is biologically involved in sensory transduction and the vision process<ref name="Human"/>. Within sensory tranduction, PPT1 is involved in the process of converting extracellular signals, such aws light, taste, touch, or smell, into electric signals that are then sent throughout the body<ref name="Human"/>. With vision, PPT1 is involved in the process of seeing images and then processing them into information that is then interpreted by the brain<ref name="Human"/>.
 ===Molecular ===
-The main molecular function of PPT1 is to breakdown lipid-modified proteins and act as a hydrolase of disulfide bonds. In the main catalytic reaction for PPT1, a cysteine residue is removed from the palmitoylated protein by PPT, resulting in a free cysteine residue and palmitoyl-CoA. It is suggested that a water molecule comes in and stabilizes the transition state, along with protonating the cysteine residue on the palmitoylated protein, allowing the palmitoyl-CoA to break free.
+The main molecular function of PPT1 is to breakdown lipid-modified proteins and act as a hydrolase of disulfide bonds<ref name="RSCB"/>. In the main catalytic reaction for PPT1, a cysteine residue is removed from the palmitoylated protein by PPT, resulting in a free cysteine residue and palmitoyl-CoA<ref name="RSCB"/>. It is suggested that a water molecule comes in and stabilizes the transition state, along with protonating the cysteine residue on the palmitoylated protein, allowing the palmitoyl-CoA to break free.
 ==Medical Relevance==
-PPT1 mutations are the root cause of several diseases, specifically those where mutations cause a decrease or depletion of PPT1. Infantile neuronal ceroid lipofuscinosis (INCF) is characterized by impaired mental and motor development, including difficulty with walking, speaking, and intellectual function, beginning around the first or second year of life<ref name="PPT">PPT1. Genetics Home Reference. U.S. National Library of Medicine, Aug. 2015.</ref>. The PPT1 mutation involved in INCF replaces an arginine with a stop signal in the instructions to make the enzyme. This mutation leads to a vast reduction in the production of PPT1, which impairs the removal of fatty acids from proteins. This impaired removal leads to fatty acid accumulations throughout the body, particularly in neuronal cells in the brain<ref name="PPT"/>. Late-infantile neuronal ceroid lipofuscinosis has the same characteristics as INCF, but the mutation varies slightly. This leads to a slight reduction in the activity of PPT1 instead of completely wiping it out.
+PPT1 mutations are the root cause of several diseases, specifically those where mutations cause a decrease or depletion of PPT1. Infantile neuronal ceroid lipofuscinosis (INCF) is characterized by impaired mental and motor development, including difficulty with walking, speaking, and intellectual function, beginning around the first or second year of life<ref name="PPT">PPT1. Genetics Home Reference. U.S. National Library of Medicine, Aug. 2015.</ref>. The PPT1 mutation involved in INCF replaces an arginine with a stop signal in the instructions to make the enzyme. This mutation leads to a vast reduction in the production of PPT1, which impairs the removal of fatty acids from proteins. This impaired removal leads to fatty acid accumulations throughout the body, particularly in neuronal cells in the brain<ref name="PPT"/>. Late-infantile neuronal ceroid lipofuscinosis has the same characteristics as INCF, but the mutation varies slightly. This leads to a slight reduction in the activity of PPT1 instead of completely wiping it out<ref name="PPT"/>.
-Mutations can also cause premature stop signals to be added to the instructions to create PPT1, resulting in Kufs disease. This is characterized by seizures, problems with movement, and a decline of intellectual function, usually beginning in early adulthood<ref name="PPT"/>. Although premature stop signals are added, these mutations allow enough PPT1 to be produced so that the onset is later on in life and the life expectancy is higher.
+Mutations can also cause premature stop signals to be added to the instructions to create PPT1, resulting in Kufs disease<ref name="PPT"/>. This is characterized by seizures, problems with movement, and a decline of intellectual function, usually beginning in early adulthood<ref name="PPT"/>. Although premature stop signals are added, these mutations allow enough PPT1 to be produced so that the onset is later on in life and the life expectancy is higher.
 </StructureSection>