User:Andrew Wills/Sandbox 1: Difference between revisions

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==Active Sites and Mechanism==

The HhH segment of AlkA connects to the phosphodiester backbone of DNA by hydrogen bonding and <scene name='56/566536/Sodium_ion_interaction/1'>sodium ion interaction</scene>. The binding of the HhH segment to DNA stabilizes the damaged base and creates a 66 degree bend away from the protein that widens the minor groove of DNA.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> <scene name='56/566536/Leu_125/2'>Leu 125</scene> fits into the minor groove between base pairs and allows the alkylated base to be flipped into the active site.<ref name="Hollis">Hollis, Thomas, Yoshitaka Ichikawa, and Tom Ellenberger. "DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA." EMBO Journal. 19.4 (2000): 758-766. Print. </ref>

The AlkA active site is located where the second and third domains are separated by a deep nonpolar cleft that is lined with the aromatic side chains Phe18, Tyr273, Trp272, Tyr222, and Trp218.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> These side chains create a <scene name='56/566536/Binding_pocket/1'>DNA Binding Pocket</scene> for the alkylated base.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> Once the damaged base is in the active site, <scene name='56/566536/Trp_272/1'>Trp272</scene> stabilizes the flipped out alkylated base in the binding pocket by aromatic ring-stacking interactions.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> Asp238 is essential for allowing the reaction to proceed, and points into the nonpolar pocket in order to allow stabilization of a carbocation intermediate. This stabilization is what allows the cleavage of the glycosidic bond on the damaged base.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> Mutation or inhibition of the Asp238 residue will prevent AlkA from performing base excision repair.

The AlkA active site is located where the second and third domains are separated by a deep nonpolar cleft that is lined with the aromatic side chains Phe18, Tyr273, Trp272, Tyr222, and Trp218.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> These side chains create a <scene name='56/566536/Binding_pocket/1'>DNA Binding Pocket</scene> for the alkylated base.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> Once the damaged base is in the active site, <scene name='56/566536/Trp_272/1'>Trp272</scene> stabilizes the flipped out alkylated base in the binding pocket by aromatic ring-stacking interactions.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> <scene name='56/566536/Asp_238/1'>Asp238</scene> is essential for allowing the reaction to proceed, and points into the nonpolar pocket in order to allow stabilization of a carbocation intermediate. This stabilization is what allows the cleavage of the glycosidic bond on the damaged base.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> Mutation or inhibition of the Asp238 residue will prevent AlkA from performing base excision repair.

==DNA Interaction==

@@ Line 17: / Line 17: @@
 ==Active Sites and Mechanism==
 The HhH segment of AlkA connects to the phosphodiester backbone of DNA by hydrogen bonding and <scene name='56/566536/Sodium_ion_interaction/1'>sodium ion interaction</scene>. The binding of the HhH segment to DNA stabilizes the damaged base and creates a 66 degree bend away from the protein that widens the minor groove of DNA.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> <scene name='56/566536/Leu_125/2'>Leu 125</scene> fits into the minor groove between base pairs and allows the alkylated base to be flipped into the active site.<ref name="Hollis">Hollis, Thomas, Yoshitaka Ichikawa, and Tom Ellenberger. "DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA." EMBO Journal. 19.4 (2000): 758-766. Print. </ref>
-The AlkA active site is located where the second and third domains are separated by a deep nonpolar cleft that is lined with the aromatic side chains Phe18, Tyr273, Trp272, Tyr222, and Trp218.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> These side chains create a <scene name='56/566536/Binding_pocket/1'>DNA Binding Pocket</scene> for the alkylated base.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> Once the damaged base is in the active site, <scene name='56/566536/Trp_272/1'>Trp272</scene> stabilizes the flipped out alkylated base in the binding pocket by aromatic ring-stacking interactions.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref>  Asp238 is essential for allowing the reaction to proceed, and points into the nonpolar pocket in order to allow stabilization of a carbocation intermediate. This stabilization is what allows the cleavage of the glycosidic bond on the damaged base.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> Mutation or inhibition of the Asp238 residue will prevent AlkA from performing  base excision repair.
+The AlkA active site is located where the second and third domains are separated by a deep nonpolar cleft that is lined with the aromatic side chains Phe18, Tyr273, Trp272, Tyr222, and Trp218.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> These side chains create a <scene name='56/566536/Binding_pocket/1'>DNA Binding Pocket</scene> for the alkylated base.<ref name="Labahn">Labahn, Jorg, Orlando Scharer, et al. "Structural Basis for the Excision Repair of Alkylation-Damaged DNA." Cell. 86.2 (1996): 321-329. Print.</ref> Once the damaged base is in the active site, <scene name='56/566536/Trp_272/1'>Trp272</scene> stabilizes the flipped out alkylated base in the binding pocket by aromatic ring-stacking interactions.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref>  <scene name='56/566536/Asp_238/1'>Asp238</scene> is essential for allowing the reaction to proceed, and points into the nonpolar pocket in order to allow stabilization of a carbocation intermediate. This stabilization is what allows the cleavage of the glycosidic bond on the damaged base.<ref name="Moe">Moe, E, D.R. Hall, et al. "Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans." Biological Crystallography. 68.6 (2012): 703-712. Print. </ref> Mutation or inhibition of the Asp238 residue will prevent AlkA from performing  base excision repair.
 ==DNA Interaction==