Sandbox Reserved 1053: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA, Ben Zercher, Geoffrey C. Hoops, Katelyn Baumer, Mary Liggett, Jakob Jozwiakowski

@@ Line 10: / Line 10: @@
 paradigm ArsR family zinc sensor in the DNA-bound state. PNAS 106:43
 -18182.</ref>. The CzrB gene in turn codes for a Zn<sup>+2</sup> pump, the [http://proteopedia.org/wiki/index.php/3byr CzrB] protein.  When relatively low amounts of zinc are present in the cell CzrA will bind to the operator on the Czr operon, preventing the progression of RNA polymerase and thus inhibiting expression of CzrB. Decreased expression of CzrB results in a buildup of Zn<sup>+2</sup> inside the cell, as there are fewer pumps to export Zn<sup>+2</sup>. This metal sensing system serves to maintain an appropriate intracellular concentration of Zn<sup>+2</sup>.
-==Structure and Mechanism of Action==
+==Structural Overview==
+Czr A functions as a [https://en.wikipedia.org/wiki/Protein_dimer dimer] to repress gene transcription.  Each <scene name='69/694218/Monomeric_unit/1'>monomeric unit</scene> contains <scene name='69/694218/Helices/1'>five alpha helices</scene> seen in purple and <scene name='69/694218/B_sheets/1'>one antiparallel beta sheet</scene> displayed in yellow. Key [https://en.wikipedia.org/wiki/Alpha_helix helices] regulate the binding of DNA versus Zn<sup>+2</sup>. The <scene name='69/694220/2kjb_colored_alpha_4/1'>α4 helices</scene> (green) are the location of DNA binding and the <scene name='69/694220/Zinc_pocket_with_residues/2'>alpha 5 helices</scene> (red) contain the Zn<sup>+2</sup> binding sites.
+==Allosteric Inhibition by Zn<sup>+2</sup>==
+CzrA is allosterically inhibited by the binding of two Zn<sup>+2</sup> ions. As Zn<sup>+2</sup> ions bind to the alpha 5 helices, the alpha 5 helices move and push the alpha 4 helices into a conformation with low affinity for DNA (Figure 2). Two separate PDB codes exist for Czr A: Czr A with DNA bound (2KJB) and Czr A with zinc<sup>+2</sup> bound (2KJC). Unfortunately, zinc ions are not visible in the 2KJC NMR structure that was obtained for Czr A.
-Czr A functions as a [https://en.wikipedia.org/wiki/Protein_dimer dimer] to repress gene transcription.  Each <scene name='69/694218/Monomeric_unit/1'>monomeric unit</scene> contains <scene name='69/694218/Helices/1'>five alpha helices</scene> seen in purple and <scene name='69/694218/B_sheets/1'>one antiparallel beta sheet</scene> displayed in yellow. Key [https://en.wikipedia.org/wiki/Alpha_helix helices] regulate the binding of DNA versus Zn<sup>+2</sup>. The <scene name='69/694220/2kjb_colored_alpha_4/1'>α4 helices</scene> (green) are the location of DNA binding and the <scene name='69/694220/Zinc_pocket_with_residues/2'>alpha 5 helices</scene> (red) contain the Zn<sup>+2</sup> binding sites. As Zn<sup>+2</sup> ions bind to the alpha 5 helices, the alpha 5 helices move and push the alpha 4 helices into a conformation with low affinity for DNA (Figure 2). Two separate PDB codes exist for Czr A: Czr A with DNA bound (2KJB) and Czr A with zinc<sup>+2</sup> bound (2KJC). Unfortunately, zinc ions are not visible in the 2KJC NMR structure that was obtained for Czr A.
 [[Image:800px-2KJB + 2KJC side by side.fw.png CROPPED.fw.png|600px|center|thumb| Figure 2: Comparison of Czr A bound to DNA to Czr A with Zn<sup>+2</sup> bound with the alpha five helices shown in red and the alpha four helices shown in green]]
-CzrA is allosterically inhibited by the binding of two Zn<sup>+2</sup> ions. CzrA displays two different conformations; the first has a high affinity for DNA and has no Zn<sup>+2</sup> ions bound to it (PDB code: 2KJB). In this conformation the <scene name='69/694220/A5_helices__dna_binding/2'>alpha 5 helices are aligned</scene>. Binding of zinc drives a conformational change (PDB code: 2KJC) in which the <scene name='69/694220/A5_helices_dna_binding/2'>alpha 5 helices become unaligned</scene>, changing the overall shape of the protein and significantly lowering its affinity for DNA (Figure 2). This allows for zinc transport to be self regulated. That is, when zinc concentration in the cell is high, zinc ions bind to Czr A, causing a conformational change which releases the bound DNA. DNA without Czr A bound is free to be transcribed and Czr B is again expressed, allowing for Zn<sup>+2</sup> transport out of the cell. At low Zn<sup>+2</sup> concentrations, Czr A represses RNA Polymerase activity, and Zn<sup>+2</sup> ions are maintained inside the cell.
+CzrA displays two different conformations; the first has a high affinity for DNA and has no Zn<sup>+2</sup> ions bound to it (PDB code: 2KJB). In this conformation the <scene name='69/694220/A5_helices__dna_binding/2'>alpha 5 helices are aligned</scene>. Binding of zinc drives a conformational change (PDB code: 2KJC) in which the <scene name='69/694220/A5_helices_dna_binding/2'>alpha 5 helices become unaligned</scene>, changing the overall shape of the protein and significantly lowering its affinity for DNA (Figure 2). This allows for zinc transport to be self regulated. That is, when zinc concentration in the cell is high, zinc ions bind to Czr A, causing a conformational change which releases the bound DNA. DNA without Czr A bound is free to be transcribed and Czr B is again expressed, allowing for Zn<sup>+2</sup> transport out of the cell. At low Zn<sup>+2</sup> concentrations, Czr A represses RNA Polymerase activity, and Zn<sup>+2</sup> ions are maintained inside the cell.