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<StructureSection load='CzrAwithDNA.pdb' size='340' frame='true' side='right' caption='The dimer Czr A' scene=''>
<StructureSection load='CzrAwithDNA.pdb' size='340' frame='true' side='right' caption='The dimer Czr A' scene=''>
<scene name='69/694220/Czra_with_dna/1'>CzrA</scene> is a transcriptional repressor protein responsible for the regulation of the Czr operon in prokaryotes.  The best studied example to date comes from ''Staphylococcus aureus''.
<scene name='69/694220/Czra_with_dna/1'>CzrA</scene> is a transcriptional repressor protein responsible for the regulation of the Czr operon in prokaryotes.  The best studied example to date comes from ''Staphylococcus aureus''.
==The Czr Operon==
==Biological Function==
===Operon Overview===
===Operon Overview===
[https://en.wikipedia.org/wiki/Operon Operons] are a critical genetic component of most prokaryotic cells. There are many different operons, responsible for the production of proteins with a wide range of functions. The most well-known and studied operons are the [https://en.wikipedia.org/wiki/Lac_operon Lac] and [https://en.wikipedia.org/wiki/Trp_operon Trp] operons, responsible for producing enzymes which metabolize lactose and tryptophan respectively. Despite many differences in each operon and the proteins that they encode, operons all function in the same general manner (Figure 1). Each operon contains a [https://en.wikipedia.org/wiki/Regulator_gene regulator], an [https://en.wikipedia.org/wiki/Operator_(biology) operator], and one or more [https://en.wikipedia.org/wiki/Structural_gene structural genes]. The regulator gene codes for a protein responsible for managing the expression level of the structural genes. The operator contains the binding sequence for [https://en.wikipedia.org/wiki/RNA_polymerase RNA polymerase] and is the site where [https://en.wikipedia.org/wiki/Transcription_(biology) transcription] begins. Lastly, the structural genes code for proteins to be used elsewhere. The regulator protein (produced as a result of expression of the regulator gene) usually acts in a repressive manner. The regulator protein will bind to the operator gene, inhibiting the binding and/or progression of RNA polymerase to the structural genes, thus inhibiting transcription of the genes into mRNA.  If the regulator protein were always active, the structural genes would never be expressed, so there must be a way to inactive the regulator protein, thus enabling expression of the structural genes. This is usually achieved through the binding of an inhibitor to the regulator protein. Since regulator proteins are DNA binding proteins, often this inhibition is [https://en.wikipedia.org/wiki/Allosteric_regulation allosteric] rather than competitive. The inhibitor of the regulator protein binds to somewhere other than the active site of the protein, changing the conformation of the regulator protein to decrease its ability to bind DNA and repress transcription.  
[https://en.wikipedia.org/wiki/Operon Operons] are a critical genetic component of most prokaryotic cells. There are many different operons, responsible for the production of proteins with a wide range of functions. The most well-known and studied operons are the [https://en.wikipedia.org/wiki/Lac_operon Lac] and [https://en.wikipedia.org/wiki/Trp_operon Trp] operons, responsible for producing enzymes which metabolize lactose and tryptophan respectively. Despite many differences in each operon and the proteins that they encode, operons all function in the same general manner (Figure 1). Each operon contains a [https://en.wikipedia.org/wiki/Regulator_gene regulator], an [https://en.wikipedia.org/wiki/Operator_(biology) operator], and one or more [https://en.wikipedia.org/wiki/Structural_gene structural genes]. The regulator gene codes for a protein responsible for managing the expression level of the structural genes. The operator contains the binding sequence for [https://en.wikipedia.org/wiki/RNA_polymerase RNA polymerase] and is the site where [https://en.wikipedia.org/wiki/Transcription_(biology) transcription] begins. Lastly, the structural genes code for proteins to be used elsewhere. The regulator protein (produced as a result of expression of the regulator gene) usually acts in a repressive manner. The regulator protein will bind to the operator gene, inhibiting the binding and/or progression of RNA polymerase to the structural genes, thus inhibiting transcription of the genes into mRNA.  If the regulator protein were always active, the structural genes would never be expressed, so there must be a way to inactive the regulator protein, thus enabling expression of the structural genes. This is usually achieved through the binding of an inhibitor to the regulator protein. Since regulator proteins are DNA binding proteins, often this inhibition is [https://en.wikipedia.org/wiki/Allosteric_regulation allosteric] rather than competitive. The inhibitor of the regulator protein binds to somewhere other than the active site of the protein, changing the conformation of the regulator protein to decrease its ability to bind DNA and repress transcription.  
[[Image:Operon.png|500px|thumb|center|Figure 1: Overview of operon structure]]
[[Image:Operon.png|500px|thumb|center|Figure 1: Overview of operon structure]]
===Czr Operon===
===The Czr Operon===
The <u>C</u>hromosome determined <u>z</u>inc <u>r</u>esponsible (Czr) operon acts as described above (Figure 1), with CzrA acting as a regulator protein to the downstream structural gene CzrB. The CzrB gene codes for a Zn<sup>+2</sup> pump, so CzrA is responsible for controlling the transport of Zn<sup>+2</sup> out of the cell. This allows CzrA to regulate the Czr operon to maintain an appropriate concentration of Zn<sup>+2</sup> inside the cell membrane.  CzrA is a transcriptional repressor protein responsible for the regulation of the Czr operon<ref name="critical">Arunkumar A., Campanello G., Giedroc D. (2009). Solution Structure of a  
The <u>C</u>hromosome determined <u>z</u>inc <u>r</u>esponsible (Czr) operon acts as described above (Figure 1), with CzrA acting as a regulator protein to the downstream structural gene CzrB<ref name="critical">Arunkumar A., Campanello G., Giedroc D. (2009). Solution Structure of a  
paradigm ArsR family zinc sensor in the DNA-bound state. PNAS 106:43  
paradigm ArsR family zinc sensor in the DNA-bound state. PNAS 106:43  
18177-18182.</ref>. The Czr operon contains genes for the proteins CzrA and [http://proteopedia.org/wiki/index.php/3byr Czr B]. Czr B is a Zinc transport protein that exports Zn<sup>+2</sup> out of the cell while Czr A regulates this process by controlling expression level of Czr B. When relatively low amounts of zinc are present in the cell Czr A will bind to the operator on the Czr operon, preventing the progression of RNA polymerase and thus inhibiting expression of Czr B. Decreased expression of Czr B results in a buildup of Zn<sup>+2</sup> inside the cell, as there are fewer pumps to export Zn<sup>+2</sup>. Because Czr A and Czr B are transcribed as part of the same operon, an inhibitor of Czr A must be readily available to allow full transcription of Czr B when necessary. Czr A is allosterically inhibited by the binding of two Zn<sup>+2</sup> ions, which is ideal in that this allows expression of Czr B to be dependent on the relative amount of Zn<sup>+2</sup> in the cell. Czr A 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.
18177-18182.</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>.
 
CzrA is allosterically inhibited by the binding of two Zn<sup>+2</sup> ions, which is ideal in that this allows expression of CzrB to be dependent on the relative amount of Zn<sup>+2</sup> in 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.
   
   
== Structural Overview ==
== Structural Overview ==

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