Sandbox Reserved 1053: Difference between revisions

Ser 54, Ser 57, and His 58 have been found to be the main <scene name='69/694219/Serandhisresidues/3'>sites of DNA interaction</scene>. <scene name='69/694220/2kjb_dna_alpha_4_helix/1'>These residues</scene> are likely to interact with the 5'-TGAA sequence found in the half-site of the DNA, where the alpha 4 helices <scene name='69/694219/Czra_with_dna/2'>form an interaction with DNA</scene>. These residues are found in the N terminal of the alpha 4 helix (figure 3). Additionally, Val 42 and Gln 53 are involved in the <scene name='69/694219/Dna_binding_pocket/1'>DNA binding pocket</scene>. This conclusion was experimentally determined by mutagenesis of the Gln and Val with Ala residues and measuring the mutant DNA binding capacity. In a previously published article <ref name="critical"/>, the DNA bound state of Czr A was tested by using the known critical residues for DNA interactions. <scene name='69/694220/Dna_binding_experiment/1'> Critical DNA binding residues</scene> Gln 53, Val 42 (red), Ser 54, Ser 57, and His 58 (orange) were individually mutated to Ala, and kinetic experiments were performed. Compared to wild type Czr A, mutating Gln53 and V42 residues resulted in an 11-fold and 160-fold decrease in K_a, respectively. Mutations to the main DNA interaction sites Ser 54, Ser 57, and His 58 resulted in binding similar to the <scene name='69/694220/Dna_residues_when_inhibited/1'>fully inhibited Zn²⁺ bound state</scene>. The conformational change that occurs from the Zinc to DNA bound state regarding these residues is small, but the alpha 4 helix (shown in green in Figure 2) does subtly move. Because no major physical change occurs between these two states, it further supports that this region is the main DNA interaction site because of the loss of affinity after the mutation took place. Table 1 in this same article shows the different K_observed, and the measured decrease in K_observed for each mutation. The bind between the DNA and the protein can be attributed to losing certain intermolecular forces such as possible hydrogen bonding when changing from Gln and Ala, and a loss of London Dispersion forces in the Val to Ala change.