Sandbox reserved 1751 - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=Sandbox_reserved_1751 Sandbox reserved 1751 - Revision history 2026-04-15T19:33:27Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644203&oldid=prev Grant Johnson at 03:23, 18 October 2022 2022-10-18T03:23:17Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:23, 18 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of <del style="color: red; font-weight: bold; text-decoration: none;">the nucleotide </del>Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/3'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644202&oldid=prev Grant Johnson at 03:22, 18 October 2022 2022-10-18T03:22:07Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:22, 18 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/<del style="color: red; font-weight: bold; text-decoration: none;">2</del>'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/5'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/<ins style="color: red; font-weight: bold; text-decoration: none;">3</ins>'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644201&oldid=prev Grant Johnson at 03:12, 18 October 2022 2022-10-18T03:12:08Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:12, 18 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<del style="color: red; font-weight: bold; text-decoration: none;">4</del>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<ins style="color: red; font-weight: bold; text-decoration: none;">5</ins>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644200&oldid=prev Grant Johnson at 03:10, 18 October 2022 2022-10-18T03:10:20Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:10, 18 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<del style="color: red; font-weight: bold; text-decoration: none;">3</del>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<ins style="color: red; font-weight: bold; text-decoration: none;">4</ins>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644199&oldid=prev Grant Johnson at 03:03, 18 October 2022 2022-10-18T03:03:19Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 03:03, 18 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/3'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s<del style="color: red; font-weight: bold; text-decoration: none;">. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA</del>. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly <del style="color: red; font-weight: bold; text-decoration: none;">from the 3' end</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">MutH must be able to correctly recognize the GATC palindrome of the damaged umethylated daughter strand in order to cleave it properly. </ins>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in <ins style="color: red; font-weight: bold; text-decoration: none;">the minor groove of the DNA. Lys45/Asp46 interacts with the phosphate backbone to narrow </ins>the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/3'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644198&oldid=prev Grant Johnson at 02:55, 18 October 2022 2022-10-18T02:55:20Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 02:55, 18 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<del style="color: red; font-weight: bold; text-decoration: none;">2</del>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<ins style="color: red; font-weight: bold; text-decoration: none;">3</ins>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <scene name='92/925551/Dek_motif/2'>DEK motif</scene>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644197&oldid=prev Grant Johnson at 02:48, 18 October 2022 2022-10-18T02:48:43Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 02:48, 18 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Structure of MutH ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Structure of MutH ==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond<del style="color: red; font-weight: bold; text-decoration: none;">. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location</del>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/2'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The <scene name='92/925551/Muth_arms/1'>C-arm</scene> is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the damaged daughter strand DNA substrate and catalyze the hydrolysis reaction in the correct location. </ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/2'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the <ins style="color: red; font-weight: bold; text-decoration: none;"><scene name='92/925551/Dek_motif/2'></ins>DEK motif<ins style="color: red; font-weight: bold; text-decoration: none;"></scene></ins>. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/2'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644111&oldid=prev Grant Johnson at 12:20, 11 October 2022 2022-10-11T12:20:19Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:20, 11 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/2'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/<del style="color: red; font-weight: bold; text-decoration: none;">1</del>'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/2'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <scene name='92/925551/Catalytic_site/<ins style="color: red; font-weight: bold; text-decoration: none;">2</ins>'>nucleophilic attack reaction</scene> to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644063&oldid=prev Grant Johnson at 06:48, 11 October 2022 2022-10-11T06:48:21Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 06:48, 11 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/2'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a nucleophilic attack reaction to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/2'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a <ins style="color: red; font-weight: bold; text-decoration: none;"><scene name='92/925551/Catalytic_site/1'></ins>nucleophilic attack reaction<ins style="color: red; font-weight: bold; text-decoration: none;"></scene> </ins>to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson http://52.214.119.220/wiki/index.php?title=Sandbox_reserved_1751&diff=3644061&oldid=prev Grant Johnson at 06:37, 11 October 2022 2022-10-11T06:37:55Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 06:37, 11 October 2022</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a <scene name='92/925551/Muth_arms/1'>"V" shape</scene>. The N arm contains the catalytic core consisting of the <scene name='92/925551/Dek_motif/2'>DEK motif</scene> and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<del style="color: red; font-weight: bold; text-decoration: none;">1</del>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a nucleophilic attack reaction to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1 Ser65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. <scene name='92/925551/Loop_67/<ins style="color: red; font-weight: bold; text-decoration: none;">2</ins>'>Loop 67</scene> (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a nucleophilic attack reaction to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></structuresection></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== References ==</div></td></tr> </table>

Grant Johnson