Sandbox Reserved 1063: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 17: | Line 17: | ||
The AdcR MarR transcriptional regulator's structure resembles that of other proteins in the MarR family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif (Figure 2) that assists in binding DNA <ref name="guerra" />. The <scene name='69/694230/Whth_4/7'>winged helix turn helix</scene> motif is made up of the <font color='blue'>α3</font> and <font color='blue'>α4 helices</font> along with <scene name='69/694230/Anti-parallel_beta_sheet/2'>anti-parallel β sheets</scene> on each side. There is one wHTH motif per monomer. The recognition helix, or the α4 helix, binds the major groove of DNA through [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions] between exposed bases <ref name="guerra" />. 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 β sheets contain several <scene name='69/694230/Positive_residues_on_wing_3/4'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA. The charge map (Figure 3) highlights the dark blue tips of the wHTH motif consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. The residues are only shown on the random loop of one monomer because the random loop on the other protein monomer <scene name='69/694230/Uncrystallized_loop/1'>was not crystallized</scene>. | The AdcR MarR transcriptional regulator's structure resembles that of other proteins in the MarR family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif (Figure 2) that assists in binding DNA <ref name="guerra" />. The <scene name='69/694230/Whth_4/7'>winged helix turn helix</scene> motif is made up of the <font color='blue'>α3</font> and <font color='blue'>α4 helices</font> along with <scene name='69/694230/Anti-parallel_beta_sheet/2'>anti-parallel β sheets</scene> on each side. There is one wHTH motif per monomer. The recognition helix, or the α4 helix, binds the major groove of DNA through [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions] between exposed bases <ref name="guerra" />. 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 β sheets contain several <scene name='69/694230/Positive_residues_on_wing_3/4'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA. The charge map (Figure 3) highlights the dark blue tips of the wHTH motif consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. The residues are only shown on the random loop of one monomer because the random loop on the other protein monomer <scene name='69/694230/Uncrystallized_loop/1'>was not crystallized</scene>. | ||
== '''Zn(II) Binding''' == | == '''Zn(II) Binding''' == | ||
Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/2_binding_sites/4'>two binding sites for zinc</scene> on each of its two protomers and can bind a total of four Zn(II) ions. The <scene name='69/694230/Alpha1-alpha2_loop/2'>α1-α2 loop</scene> combined with the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> and <scene name='69/694230/Alpha_2/1'>α2 helix</scene> make up the <scene name='69/694230/Two_binding_sites/2'>metal binding sites</scene>. Each protomer has one high affinity site (Binding site 1; KZn<sub>1</sub> = 10<sup>12</sup> M; pH 8) and one low affinity binding site (Binding Site 2; KZn<sub>2</sub> = 10<sup>7</sup> M; pH 8) <ref name="Reyes">PMID:20804771</ref>. | Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/2_binding_sites/4'>two binding sites for zinc</scene> on each of its two protomers and can bind a total of four Zn(II) ions. The <scene name='69/694230/Alpha1-alpha2_loop/2'>α1-α2 loop</scene> combined with the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> and <scene name='69/694230/Alpha_2/1'>α2 helix</scene> make up the <scene name='69/694230/Two_binding_sites/2'>metal binding sites</scene>. Each protomer has one high affinity site (Binding site 1; KZn<sub>1</sub> = 10<sup>12</sup> M; pH 8) and one low affinity binding site (Binding Site 2; KZn<sub>2</sub> = 10<sup>7</sup> M; pH 8) <ref name="Reyes">PMID:20804771</ref>. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/5'>hydrogen bonding</scene> of H108 and E41. | ||
=== Binding Site 1 === | === Binding Site 1 === | ||
<scene name='69/694230/Binding_site_1/5'>Binding site 1</scene> consists of a distorted tetrahedral geometry around Zn(II). The four amino acids involved in zinc binding are E24, H42, H108, and H112. Binding site 1 is the only binding site that plays a significant role in the protein's regulatory function. The ability of binding site 1 to coordinate to the Zn(II) ion is pH dependent. At pH 6 the binding affinity for the Zn(II) ion is 10<sup>9</sup> - 10<sup>10</sup> M<sup>-1</sup>, but at pH 8 the binding affinity increases to 10<sup>12</sup> M<sup>-1</sup> <ref name="Reyes" />. This is due to the charges on the histidines of the binding site. At pH 6, the histidines are positively charged and are not able to interact with the positively charged Zn(II) ion. However, at pH 8 the histidines are neutrally charged and are able to coordinate with Zn(II), which increases the overall binding affinity. The AdcR MarR transcriptional regulator is able to bind Co(II) in binding site 1 in a way that induces similar conformational changes to Zn(II) binding. Co(II) coordination in binding site 1 is able to allosterically activate DNA binding similarly to Zn(II) binding <ref name="guerra" />. | <scene name='69/694230/Binding_site_1/5'>Binding site 1</scene> consists of a distorted tetrahedral geometry around Zn(II). The four amino acids involved in zinc binding are E24, H42, H108, and H112. Binding site 1 is the only binding site that plays a significant role in the protein's regulatory function. The ability of binding site 1 to coordinate to the Zn(II) ion is pH dependent. At pH 6 the binding affinity for the Zn(II) ion is 10<sup>9</sup> - 10<sup>10</sup> M<sup>-1</sup>, but at pH 8 the binding affinity increases to 10<sup>12</sup> M<sup>-1</sup> <ref name="Reyes" />. This is due to the charges on the histidines of the binding site. At pH 6, the histidines are positively charged and are not able to interact with the positively charged Zn(II) ion. However, at pH 8 the histidines are neutrally charged and are able to coordinate with Zn(II), which increases the overall binding affinity. The AdcR MarR transcriptional regulator is able to bind Co(II) in binding site 1 in a way that induces similar conformational changes to Zn(II) binding. Co(II) coordination in binding site 1 is able to allosterically activate DNA binding similarly to Zn(II) binding <ref name="guerra" />. | ||