Sandbox Reserved 1063: Difference between revisions
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==='''Structural Overview'''=== | ==='''Structural Overview'''=== | ||
[[Image:Screen Shot 2017-04-18 at 11.56.32 PM.png|300 px|right|thumb|'''Figure 2'''. A generic protein representing the [https://images.google.com/imgres?imgurl=https%3A%2F%2Fclassconnection.s3.amazonaws.com%2F838%2Fflashcards%2F2220838%2Fjpg%2Fasdf-144940F88BA53A918F3.jpg&imgrefurl=https%3A%2F%2Fwww.studyblue.com%2Fnotes%2Fnote%2Fn%2Flecture-13%2Fdeck%2F10226974&docid=qBvv1vgKeLTGcM&tbnid=3nuaRjPWKUBfqM%3A&vet=1&w=741&h=756&hl=en&source=sh%2Fx%2Fim wHTH] motif binding the major and minor groove of DNA similar to AdcR.]] | |||
One of the two functional domains of AdcR is the <scene name='69/694230/Dimerization_domain/3'> dimerization domain</scene>. This domain connects and stabilizes the two pseudosymmetric protomers and is composed of the <scene name='69/694230/Alpha_1/1'>α1 helix</scene>, the <scene name='69/694230/Alpha_6/1'>α6 helix</scene> . and the C-terminus of the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> . This domain is connected to the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain] by the long α5 helix. The DNA binding domain interacts with the major and minor grooves of DNA via the <scene name='69/694230/Whth_4/7'>winged helix-turn-helix (wHTH)</scene> motif. The binding of Zinc to the <scene name='69/694230/2_binding_sites/4'>Zinc binding pocket</scene> induces a conformational change that allows for a <scene name='69/694230/Hydrogen_bonding_1/4'>hydrogen bond network</scene> between 4 specific residues. This network connects multiple helices from the metal binding pockets and DNA binding domain, and is believed play a critical role in the allosteric activation of AdcR, allowing the protein to bind exposed bases along the major and minor grooves of the DNA ligand <ref name="guerra">PMID:22085181</ref>. Thus, the protein is able to perform its biological function by activating transcription after binding DNA. | One of the two functional domains of AdcR is the <scene name='69/694230/Dimerization_domain/3'> dimerization domain</scene>. This domain connects and stabilizes the two pseudosymmetric protomers and is composed of the <scene name='69/694230/Alpha_1/1'>α1 helix</scene>, the <scene name='69/694230/Alpha_6/1'>α6 helix</scene> . and the C-terminus of the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> . This domain is connected to the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain] by the long α5 helix. The DNA binding domain interacts with the major and minor grooves of DNA via the <scene name='69/694230/Whth_4/7'>winged helix-turn-helix (wHTH)</scene> motif. The binding of Zinc to the <scene name='69/694230/2_binding_sites/4'>Zinc binding pocket</scene> induces a conformational change that allows for a <scene name='69/694230/Hydrogen_bonding_1/4'>hydrogen bond network</scene> between 4 specific residues. This network connects multiple helices from the metal binding pockets and DNA binding domain, and is believed play a critical role in the allosteric activation of AdcR, allowing the protein to bind exposed bases along the major and minor grooves of the DNA ligand <ref name="guerra">PMID:22085181</ref>. Thus, the protein is able to perform its biological function by activating transcription after binding DNA. | ||
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== '''DNA Binding''' == | == '''DNA Binding''' == | ||
=== Helix-Turn-Helix Motif === | === Helix-Turn-Helix Motif === | ||
[[Image: | [[Image:Charge_map.jpg |300 px|right|thumb|'''Figure 3'''. A charge map of AdcR shows the general triangular shape and the <font color='blue'>positively</font> charged area on the tips of the wHTH motif]] | ||
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>. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/5'>hydrogen bonding</scene> of H108 and E41. | 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. | ||