User:Asif Hossain/Sandbox 1: Difference between revisions

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===Key Residues===

The <scene name='81/811085/Active_site/13'>active site</scene> of HDAC8 is composed of 2 catalytic dyads: <scene name='81/811085/Dyads/3'>His143/Asp183 and His142/Asp176</scene>, which activate the catalytic water nucleophile. A Tyr306, through mutation to Phe in the pdb file 2v5w (modeled in the overall view) was observed to render the protein mostly inactive. Thus, it has been hypothesized that the this residue is critical for stabilization of the transition state with the Zn2+ ion. This mutation allowed the determination of the crystal structure of HDAC8 in complex with the ligand. <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref>

The <scene name='81/811085/Active_site/13'>active site</scene> of HDAC8 is composed of 2 catalytic dyads: <scene name='81/811085/Dyads/5'>His143/Asp183 and His142/Asp176</scene>, which activate the catalytic water nucleophile. A Tyr306, through mutation to Phe in the pdb file 2v5w (modeled in the overall view) was observed to render the protein mostly inactive. Thus, it has been hypothesized that the this residue is critical for stabilization of the transition state with the Zn2+ ion. This mutation allowed the determination of the crystal structure of HDAC8 in complex with the ligand. <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref>

===Binding Pocket===

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==Mechanism==

Once the substrate is bound to the binding pocket through interactions with <scene name='81/811087/Ligand_interaction/2'>Asp101, Phe152 and Phe208</scene>, the water molecule attacks the carbonyl carbon of the ε-amino-lysine sidechain of N-terminal core of histone proteins (Figure 2). This water molecule is recruited and stabilized by <scene name='81/811085/Dyads/3'>two catalytic dyads</scene>. The first dyad consists of His143 and Asp183. Asp183 interacts with His143 to shift electron density so that His143 may act as a general base to remove a proton from water. The second catalytic dyad consists of His142 and Asp176 and stabilizes the now deprotonated water molecule. A Zn2+ ion also makes the water more acidic making it a better nucleophile. The tetrahedral intermediate is stabilized by the Zn2+ ion as well as Tyr306. The amine group of the substrate's lysine acts as a general base and deprotonates His143. This drives the tetrahedral intermediate to collapse and expel the acetyl group to produce an acetate ion and a deacetylated lysine residue. <ref name="Seto, E., & Yoshida, M."> Seto, E., & Yoshida, M. (2014). Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harbor perspectives in biology, 6(4), a018713. https://doi.org/10.1101/cshperspect.a018713 </ref>

Once the substrate is bound to the binding pocket through interactions with <scene name='81/811087/Ligand_interaction/2'>Asp101, Phe152 and Phe208</scene>, the water molecule attacks the carbonyl carbon of the ε-amino-lysine sidechain of N-terminal core of histone proteins (Figure 2). This water molecule is recruited and stabilized by <scene name='81/811085/Dyads/5'>two catalytic dyads</scene>. The first dyad consists of His143 and Asp183. Asp183 interacts with His143 to shift electron density so that His143 may act as a general base to remove a proton from water. The second catalytic dyad consists of His142 and Asp176 and stabilizes the now deprotonated water molecule. A Zn2+ ion also makes the water more acidic making it a better nucleophile. The tetrahedral intermediate is stabilized by the Zn2+ ion as well as Tyr306. The amine group of the substrate's lysine acts as a general base and deprotonates His143. This drives the tetrahedral intermediate to collapse and expel the acetyl group to produce an acetate ion and a deacetylated lysine residue. <ref name="Seto, E., & Yoshida, M."> Seto, E., & Yoshida, M. (2014). Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harbor perspectives in biology, 6(4), a018713. https://doi.org/10.1101/cshperspect.a018713 </ref>

[[Image:Mech.PNG|800px||center||thumb|Figure 2: HDAC8 Mechanism: Tyr306 was mutated to Phe306 to determine the crystal structure in the pdb file 2v5w.]]

@@ Line 21: / Line 21: @@
 ===Key Residues===
-The <scene name='81/811085/Active_site/13'>active site</scene> of HDAC8 is composed of 2 catalytic dyads: <scene name='81/811085/Dyads/3'>His143/Asp183 and His142/Asp176</scene>, which activate the catalytic water nucleophile. A Tyr306, through mutation to Phe in the pdb file 2v5w (modeled in the overall view) was observed to render the protein mostly inactive. Thus, it has been hypothesized that the this residue is critical for stabilization of the transition state with the Zn<sup>2+</sup> ion. This mutation allowed the determination of the crystal structure of HDAC8 in complex with the ligand. <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref>
+The <scene name='81/811085/Active_site/13'>active site</scene> of HDAC8 is composed of 2 catalytic dyads: <scene name='81/811085/Dyads/5'>His143/Asp183 and His142/Asp176</scene>, which activate the catalytic water nucleophile. A Tyr306, through mutation to Phe in the pdb file 2v5w (modeled in the overall view) was observed to render the protein mostly inactive. Thus, it has been hypothesized that the this residue is critical for stabilization of the transition state with the Zn<sup>2+</sup> ion. This mutation allowed the determination of the crystal structure of HDAC8 in complex with the ligand. <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref>
 ===Binding Pocket===
@@ Line 37: / Line 37: @@
 ==Mechanism==
-Once the substrate is bound to the binding pocket through interactions with <scene name='81/811087/Ligand_interaction/2'>Asp101, Phe152 and Phe208</scene>, the water molecule attacks the carbonyl carbon of the ε-amino-lysine sidechain of N-terminal core of histone proteins (Figure 2). This water molecule is recruited and stabilized by <scene name='81/811085/Dyads/3'>two catalytic dyads</scene>. The first dyad consists of His143 and Asp183. Asp183 interacts with His143 to shift electron density so that His143 may act as a general base to remove a proton from water. The second catalytic dyad consists of His142 and Asp176 and stabilizes the now deprotonated water molecule. A Zn<sup>2+</sup> ion also makes the water more acidic making it a better nucleophile. The tetrahedral intermediate is stabilized by the Zn<sup>2+</sup> ion as well as Tyr306. The amine group of the substrate's lysine acts as a general base and deprotonates His143. This drives the tetrahedral intermediate to collapse and expel the acetyl group to produce an acetate ion and a deacetylated lysine residue. <ref name="Seto, E., & Yoshida, M."> Seto, E., & Yoshida, M. (2014). Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harbor perspectives in biology, 6(4), a018713. https://doi.org/10.1101/cshperspect.a018713 </ref>
+Once the substrate is bound to the binding pocket through interactions with <scene name='81/811087/Ligand_interaction/2'>Asp101, Phe152 and Phe208</scene>, the water molecule attacks the carbonyl carbon of the ε-amino-lysine sidechain of N-terminal core of histone proteins (Figure 2). This water molecule is recruited and stabilized by <scene name='81/811085/Dyads/5'>two catalytic dyads</scene>. The first dyad consists of His143 and Asp183. Asp183 interacts with His143 to shift electron density so that His143 may act as a general base to remove a proton from water. The second catalytic dyad consists of His142 and Asp176 and stabilizes the now deprotonated water molecule. A Zn<sup>2+</sup> ion also makes the water more acidic making it a better nucleophile. The tetrahedral intermediate is stabilized by the Zn<sup>2+</sup> ion as well as Tyr306. The amine group of the substrate's lysine acts as a general base and deprotonates His143. This drives the tetrahedral intermediate to collapse and expel the acetyl group to produce an acetate ion and a deacetylated lysine residue. <ref name="Seto, E., & Yoshida, M."> Seto, E., & Yoshida, M. (2014). Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harbor perspectives in biology, 6(4), a018713. https://doi.org/10.1101/cshperspect.a018713 </ref>
 [[Image:Mech.PNG|800px||center||thumb|Figure 2: HDAC8 Mechanism: Tyr306 was mutated to Phe306 to determine the crystal structure in the pdb file 2v5w.]]