ToxT: Difference between revisions

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==Other Structural Features==

ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (helix in blue, turn in teal). <ref name="arac">PMID: 11282467</ref> The two HTH regions are linked by a very polar alpha helix (shown in black). The overall domain is composed of seven alpha helices, and is located at the C-terminus.<ref name="structure">PMID: 20133655</ref>

DNA-binding. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (helix in blue, turn in teal). <ref name="arac">PMID: 11282467</ref> The two HTH regions are linked by a very polar alpha helix (shown in black). The overall domain is composed of seven alpha helices, and is located at the C-terminus.<ref name="structure">PMID: 20133655</ref>

<scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is largely made up of residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The cis-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230. This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT. The

Ligand-binding. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is largely made up of residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The cis-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230. This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT. The

Specifically, the cis-palmitoleate appears to bind directly to ToxT, change its conformation, and thus lower the ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. Here, binding of PAM brings K31 and K230 together and essentially closes off ToxT. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, the two lysine residues repel each other and give ToxT an open conformation, allowing it to bind DNA.<ref name="structure">PMID: 20133655</ref>

Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495

Dimerization. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495

</ref> The preferred state of ToxT varies between promoters, but binding to the ctx promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]

</StructureSection>

==References==

@@ Line 7: / Line 7: @@
 ==Other Structural Features==
-ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (helix in blue, turn in teal). <ref name="arac">PMID: 11282467</ref> The two HTH regions are linked by a very polar alpha helix (shown in black). The overall domain is composed of seven alpha helices, and is located at the C-terminus.<ref name="structure">PMID: 20133655</ref>
+<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (helix in blue, turn in teal). <ref name="arac">PMID: 11282467</ref> The two HTH regions are linked by a very polar alpha helix (shown in black). The overall domain is composed of seven alpha helices, and is located at the C-terminus.<ref name="structure">PMID: 20133655</ref>
 <br/>
 <br/>
-<scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is largely made up of residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230. This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT. The
+<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is largely made up of residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230. This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT. The
 Specifically, the <i>cis</i>-palmitoleate appears to bind directly to ToxT, change its conformation, and thus lower the ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. Here, binding of PAM brings K31 and K230 together and essentially closes off ToxT. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, the two lysine residues repel each other and give ToxT an open conformation, allowing it to bind DNA.<ref name="structure">PMID: 20133655</ref>
 <br/>
 <br/>
-Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495
+<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495
 </ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]
 </StructureSection>
 ==References==
 <references/>

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