Sandbox Reserved 1063: Difference between revisions
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The AdcR MarR transcriptional regulator's structure resembles the other proteins in the same family as mentioned before; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA. This motif is characteristic of the MarR family and found within the DNA binding domain of the protein. The major groove of DNA is bound to the recognition helix while the wings of the motif grip onto the minor grooves of DNA <ref>PMID:22085181</ref>. Although AdcR is a highly alpha helical protein, the "wings" of the wHTH motif consist of two anti parallel beta strands that are made up of positively charged residues. | The AdcR MarR transcriptional regulator's structure resembles the other proteins in the same family as mentioned before; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA. This motif is characteristic of the MarR family and found within the DNA binding domain of the protein. The major groove of DNA is bound to the recognition helix while the wings of the motif grip onto the minor grooves of DNA <ref>PMID:22085181</ref>. Although AdcR is a highly alpha helical protein, the "wings" of the wHTH motif consist of two anti parallel beta strands that are made up of positively charged residues. | ||
The <scene name='69/694230/Whth_2/1'>winged helix-turn-helix</scene> motif is made up of the <font color='blue'>alpha 2</font> and <font color='blue'>alpha 4 helices</font> along with <scene name='69/694230/Anti-parallel_beta_sheet/1'>anti-parallel beta sheets</scene> on each side. Only one monomer is shown for clarity purposes. There is one wHTH motif per monomer. The recognition helix, or the alpha 4 helix, binds the major groove of DNA through hydrogen bonding and Van der Waals interactions between exposed bases. The wings of the helix bind the minor groove of DNA while the other helices stabilize the DNA and Protein upon binding. The two anti parallel beta sheets contain several <scene name='69/694230/Positive_residues_on_wing/ | The <scene name='69/694230/Whth_2/1'>winged helix-turn-helix</scene> motif is made up of the <font color='blue'>alpha 2</font> and <font color='blue'>alpha 4 helices</font> along with <scene name='69/694230/Anti-parallel_beta_sheet/1'>anti-parallel beta sheets</scene> on each side. Only one monomer is shown for clarity purposes. There is one wHTH motif per monomer. The recognition helix, or the alpha 4 helix, binds the major groove of DNA through hydrogen bonding and Van der Waals interactions between exposed bases. The wings of the helix bind the minor groove of DNA while the other helices stabilize the DNA and Protein upon binding. The two anti parallel beta sheets contain several <scene name='69/694230/Positive_residues_on_wing/5'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA. The charge map down below highlights the dark blue tips consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. | ||
[[Image:Charge_map.jpg |300 px|right|thumb| A charge map of AdcR shows the general triangular shape and the positive charged (blue) area on HTH domains]] | [[Image:Charge_map.jpg |300 px|right|thumb| A charge map of AdcR shows the general triangular shape and the positive charged (blue) area on HTH domains]] | ||