Sandbox Reserved 1852: Difference between revisions
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==General Structure== | ==General Structure== | ||
[[Image:Diels-AlderaseSurfaces.png|300px|left|thumb|Figure 3. Binding pocket and substrate. Shown is the binding pocket of the enzyme shown as surface, highlighting the electrostatics of the two catalytic residues, Tyr134 and Glu208. The ligand is color coded based on original structure: the | [[Image:Diels-AlderaseSurfaces.png|300px|left|thumb|Figure 3. Binding pocket and substrate. Shown is the binding pocket of the enzyme shown as surface, highlighting the electrostatics of the two catalytic residues, Tyr134 and Glu208. The ligand is color coded based on original structure: the dieophile is in yellow and the diene is in green. The reaction proceeds via attack of the C6 on the C5, shifting electron density to C2, which attacks C1.]] | ||
====Scaffold==== | ====Scaffold==== | ||
After early Rosetta computational modelling, an ideal protein <scene name='10/1075254/Squidscaffold/ | After early Rosetta computational modelling, an ideal protein <scene name='10/1075254/Squidscaffold/2'>scaffold</scene> was found in the 6-bladed [https://en.wikipedia.org/wiki/Beta-propeller beta-propeller] of ''Loligo vulgalis,'' or the European Squid. <ref name="Siegel"/><ref name="Scharff">PMID:11435114</ref> The protein is relatively simple, with only one chain, one unit, 324 residues, and no extra ligands, metal ions, or small molecules bound. | ||
====Active Site==== | ====Active Site==== | ||
In the designed active site, <scene name='10/1075254/Active_site/ | In the designed active site, <scene name='10/1075254/Active_site/6'>two catalytic residues</scene> stabilize the transition state of the Diels-Alder reaction. The Tyr134 acts as a <scene name='10/1075253/Y134_h_donation/1'>hydrogen bond donor</scene> to the oxygen on the dienophile (see Fig. 3). Q208 acts as a <scene name='10/1075254/208_bond_donor/1'>hydrogen bond acceptor</scene> to the nitrogen on the diene. These interactions help reduce the energetic gap between orbitals allowing the reaction to proceed. | ||
====Helix Cap==== | ====Helix Cap==== | ||
In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/1075252/Alpha_helix_highlighted/4'>motif</scene> to the top of the binding site. The hydrophobic helix “functions as a lid to constrain the substrates in a productive orientation for reaction,” decreasing the ''K<sub>m</sub>'' of the enzyme and increasing the catalytic efficiency, as seen in the measured kinetics of the enzyme.<ref name="Eiben">PMID:22267011</ref> | In the evolution process, a 16-residue [https://proteopedia.org/wiki/index.php/Alpha_helix alpha-helix] <scene name='10/1075252/Alpha_helix_highlighted/4'>motif</scene> to the top of the binding site. The hydrophobic helix “functions as a lid to constrain the substrates in a productive orientation for reaction,” decreasing the ''K<sub>m</sub>'' of the enzyme and increasing the catalytic efficiency, as seen in the measured kinetics of the enzyme.<ref name="Eiben">PMID:22267011</ref> | ||
