Sandbox Reserved 773: Difference between revisions
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== Cofactor and Substrate Binding Pocket == | == Cofactor and Substrate Binding Pocket == | ||
[[Image:Histidine Decarboxylase Binding Site.png|thumb|Figure | [[Image:Histidine Decarboxylase Binding Site.png|thumb|Figure 3. Interactions between enzyme HDC and cofactor-substrate PLP-HME at the binding site <ref name=jbc/>.]] | ||
The binding pocket for the cofactor PLP and the substrate histidine is located at the large domain. Since Histidine methyl ester (HME) is a substrate analog, PLP-HME can be utilized to demonstrate the binding interaction for the substrate-enzyme transition state at the active site <ref name=jbc/> <ref name=inhibition>PMID:850236</ref>. A one-dimensional representation of PLP-HME residing in the binding pocket can be seen in Figure 3. The hydrophobic pocket of the active site are produced by several hydrophobic amino acids including Trp-72, Tyr-80, Leu-102, Phe-104, Ala-275, Tyr-334, Ile-436 (Figure 3). This hydrophobic pocket allow for the substrate to be protected from the solvent during the catalytic reaction. | The binding pocket for the cofactor PLP and the substrate histidine is located at the large domain. Since Histidine methyl ester (HME) is a substrate analog, PLP-HME can be utilized to demonstrate the binding interaction for the substrate-enzyme transition state at the active site <ref name=jbc/> <ref name=inhibition>PMID:850236</ref>. A one-dimensional representation of PLP-HME residing in the binding pocket can be seen in Figure 3. The hydrophobic pocket of the active site are produced by several hydrophobic amino acids including Trp-72, Tyr-80, Leu-102, Phe-104, Ala-275, Tyr-334, Ile-436 (Figure 3). This hydrophobic pocket allow for the substrate to be protected from the solvent during the catalytic reaction. | ||
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A loop region appears between the residues 330 to 340 of the large domain <ref name=jbc/>. This loop protrudes from the large domain into the active site of another subunit of the dimer and makes up the entrance of the active site. Especially Tyr-334, which directly interacts with the backbone of Ser-195 through a fairly weak hydrogen bond <ref name=jbc/>. Due to the weak hydrogen bonding, the loop’s position is not rigidly fixed. Thus, this causes this loop to be fairly flexible enabling it to act as a gate to “open” or “close” the active site <ref name=jbc/>. | A loop region appears between the residues 330 to 340 of the large domain <ref name=jbc/>. This loop protrudes from the large domain into the active site of another subunit of the dimer and makes up the entrance of the active site. Especially Tyr-334, which directly interacts with the backbone of Ser-195 through a fairly weak hydrogen bond <ref name=jbc/>. Due to the weak hydrogen bonding, the loop’s position is not rigidly fixed. Thus, this causes this loop to be fairly flexible enabling it to act as a gate to “open” or “close” the active site <ref name=jbc/>. | ||
== Enzymatic Mechanism == | == Enzymatic Mechanism == | ||
