Sandbox Reserved 1475: Difference between revisions
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[[Image:Figure 3.png|thumb|upright=1.5| [[Figure 3]] Section (a) is the dimer of RalDH2 with the green spheres representing the amino and carboy termini of the substrate access channel loop. Section (b) shows the same orientation as section (a) with both dimers present and then the two dimers spun 90 degrees on the X-axis.<ref name="Lamb AL, Newcomber ME" /> ]] | [[Image:Figure 3.png|thumb|upright=1.5| [[Figure 3]] Section (a) is the dimer of RalDH2 with the green spheres representing the amino and carboy termini of the substrate access channel loop. Section (b) shows the same orientation as section (a) with both dimers present and then the two dimers spun 90 degrees on the X-axis.<ref name="Lamb AL, Newcomber ME" /> ]] | ||
The structure was based on the mitochondrial aldehyde dehydrogenase type two. RalDH2 in a monomer made up of 3 domains: a nucleotide-binding domain (1-136, 161-270), a catalytic domain (271-484), and a tetramerization domain (137-160, 485-484) as shown in | The structure was based on the mitochondrial aldehyde dehydrogenase type two. RalDH2 in a monomer made up of 3 domains: a nucleotide-binding domain (1-136, 161-270), a catalytic domain (271-484), and a tetramerization domain (137-160, 485-484) as shown in [[Figure 1]].<ref name="Lamb AL, Newcomber ME" /> | ||
The tetramer can be envisioned as an "X", with nucleotide-binding sites at the tips of the "X", and the tetramerization domains as the equatorial portion of the "X" as seen in [[Figure 2]].<ref name="Lamb AL, Newcomber ME" /> The <scene name='80/800654/1st_dimerization/1'>1st dimerization</scene> is presented by the alpha1 helix and beta11 strand of one nucleotide-binding domain, with the same alpha1 helix and beta11 strand of it's dimer ([[Figure 2]], the purple highlighted region). Although the beta strands are far apart, ordered water molecules are present to create beta-sheet contacts.<ref name="Lamb AL, Newcomber ME" /> The <scene name='80/800654/2nd_dimerization/1'>2nd Dimerization</scene> is presented by the beta18 of the catalytic domain beta-sheet of one monomer and the beta19 of the tetramerization domain of it's dimer([[Figure 2]], the pink highlighted region).<ref name="Lamb AL, Newcomber ME" /> This dimerization interaction creates an "embrace" between the beta-sheet's contact, and creates a channel for the substrate to access the active site.<ref name="Lamb AL, Newcomber ME" /> | The tetramer can be envisioned as an "X", with nucleotide-binding sites at the tips of the "X", and the tetramerization domains as the equatorial portion of the "X" as seen in [[Figure 2]].<ref name="Lamb AL, Newcomber ME" /> The <scene name='80/800654/1st_dimerization/1'>1st dimerization</scene> is presented by the alpha1 helix and beta11 strand of one nucleotide-binding domain, with the same alpha1 helix and beta11 strand of it's dimer ([[Figure 2]], the purple highlighted region). Although the beta strands are far apart, ordered water molecules are present to create beta-sheet contacts.<ref name="Lamb AL, Newcomber ME" /> The <scene name='80/800654/2nd_dimerization/1'>2nd Dimerization</scene> is presented by the beta18 of the catalytic domain beta-sheet of one monomer and the beta19 of the tetramerization domain of it's dimer([[Figure 2]], the pink highlighted region).<ref name="Lamb AL, Newcomber ME" /> This dimerization interaction creates an "embrace" between the beta-sheet's contact, and creates a channel for the substrate to access the active site.<ref name="Lamb AL, Newcomber ME" /> | ||
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===Cys-302=== | ===Cys-302=== | ||
In [[Figure 3]] it is possible to see the active site, which is where the substrate interacts with Cys-302. The Cys-302 residue acts as a nucleophilic active site on each domain as a hydrogen-bond turn that is enclosed deep inside the substrate access channel. This is where the large substrate molecules can gain access to the catalytic Cys-302. | In [[Figure 3]] it is possible to see the active site, which is where the substrate interacts with Cys-302. The Cys-302 residue acts as a nucleophilic active site on each domain as a hydrogen-bond turn that is enclosed deep inside the substrate access channel. This is where the large substrate molecules can gain access to the catalytic Cys-302. The side chain of Cys-302 is the nucleophile that attaches to the substrate retinol (at its carbonyl) when it is deprotonated. To get Cys-302 deprotonated, the amino acid Glu-268 is needed as the proton acceptor. The amine backbone of Glu-268 helps stabilize the negatively charged transition state, which helps the enzyme result in an energetically favorable conformation. Asn-187 is also used as a transition site stabilizer and is on all four domains. It worked in a similar fashion as Glu-268, in that Asn-187 amine backbone is used to stabilize the negatively charged transition state. <ref name="Analysis of Catalytic Residues in Enzyme Active Sites">J Mol Biol 324:105-121 </ref> | ||
