Sandbox Reserved 1475: Difference between revisions

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 crystal structure was cocrystallized with <scene name='80/800654/Nad/1'>NAD</scene>, and was determined at a 2.7 Angstrom resolution ([[Figure 2]] Chain D present with NAD represented in pink).<ref name="Lamb AL, Newcomber ME" /> NAD+ acts as a cofactor and is the electron acceptor in RalDH2 oxidoructase reaction as seen in the reaction presented above. RalDH2 has to be folded in a proper manner for its enzymatic function to occur. The folding of the enzyme is partially due to the interactions of NAD+ and Chloride ions. When NAD+ is present hydrogen bonds with Glu and Ser form, van der Waals interactions with non-polar residues and one polar residue (Lys) forms. The interaction with Lys-192 provides the transition state stability, making for a favorable confirmation.<ref name="Lamb AL, Newcomber ME" /> This conformational change is important since in the absence of NAD+, no crystal structures grew in any of the screened conditions. <ref></ref> The Chloride ions participate in hydrophobic interactions with Arg which also help maintain the folded structure.<ref name="Lamb AL, Newcomber ME" /> With the cofactor NAD+ present the catalytic domain of RalDH2 is highly mobile and needs the selective substrate present to immobilize the catalytic domain.