Sandbox Reserved 773: Difference between revisions
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[[Image:Histidine decarboxylase mechanism.svg.png|center]] | [[Image:Histidine decarboxylase mechanism.svg.png|center]] | ||
[[Image:Histidine decarboxylase 3D binding site.png|thumb|left|Figure 4. Structure of HDC dimer with PLP and HME. Subunit A is shown in blue, Subunit B is shown in green, and the PLP-HME is shown in orange <ref name=jbc/>.]] | |||
The substrate L-histidine is proposed to enter from the gate constructed by 5 hydrophobic residues (Tyr-80, Phe-104, Tyr-334, Leu-335, and Leu-353) along with PLP <ref name=jbc/>. This gate is compose of a very flexible loop structure which “closes” upon the entering of the substrate. This phenomenon could be explained by the hydrophobic effect, which compacts the flexible hydrophobic entrance towards the hydrophobic binding site, thereby trapping the substrate inside the catalytic region. As shown in Figure 3, the ester group of HME is located immediate to the entrance. Since the hydrophobic gate separates the solvent from the methyl ester of HME, it appears to facilitate the conversion of carboxylate group to the less hydrophilic CO2 product during catalysis <ref name=jbc/>. | The substrate L-histidine is proposed to enter from the gate constructed by 5 hydrophobic residues (Tyr-80, Phe-104, Tyr-334, Leu-335, and Leu-353) along with PLP <ref name=jbc/>. This gate is compose of a very flexible loop structure which “closes” upon the entering of the substrate. This phenomenon could be explained by the hydrophobic effect, which compacts the flexible hydrophobic entrance towards the hydrophobic binding site, thereby trapping the substrate inside the catalytic region. As shown in Figure 3, the ester group of HME is located immediate to the entrance. Since the hydrophobic gate separates the solvent from the methyl ester of HME, it appears to facilitate the conversion of carboxylate group to the less hydrophilic CO2 product during catalysis <ref name=jbc/>. | ||
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The substrate specificity of HDC mechanism involves the residue Ser-354. Due to the Van der Waal effect of its hydroxyl side chain, Ser-354 avoids other 6-membered ring amino acid such as tyrosine from entering the substrate binding pocket. With this specificity, Ser-354 only allow for the 5-membered ring histidine to be involved in the binding site during catalysis <ref name=jbc/>. | The substrate specificity of HDC mechanism involves the residue Ser-354. Due to the Van der Waal effect of its hydroxyl side chain, Ser-354 avoids other 6-membered ring amino acid such as tyrosine from entering the substrate binding pocket. With this specificity, Ser-354 only allow for the 5-membered ring histidine to be involved in the binding site during catalysis <ref name=jbc/>. | ||
The numerous hydrogen bond interaction between the enzyme and PLP restrict the translation of the substrate or cofactor. In addition, the negative charges of phosphate group of PLP is stabilized by dipole moment from the neighboring N-terminus of the helix α5 seen in Figure 4 <ref name=jbc/>. These hydrogen bonding and stability effect assist in creating an environment for PLP to stay in place during the transitional state. | The numerous hydrogen bond interaction between the enzyme and PLP restrict the translation of the substrate or cofactor. In addition, the negative charges of phosphate group of PLP is stabilized by dipole moment from the neighboring N-terminus of the helix α5 seen in Figure 4 <ref name=jbc/>. These hydrogen bonding and stability effect assist in creating an environment for PLP to stay in place during the transitional state. | ||
