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/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 interacting 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 interacting 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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 ===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/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 interacting 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 interacting 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===