User:Andrew Wills/Sandbox 1: Difference between revisions

Line 12:

==Key Structures==

AlkA is composed of three main domains with dimensions of approximately 50 Angstroms, 45 Angstroms, and 25 Angstroms.<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> The first domain (residues 1-112) is the <scene name='56/566536/N_terminal_domain_and_dna/1'>N-terminal domain</scene> that is composed of a five stranded antiparallel beta sheet and two alpha helices.<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> The <scene name='56/566536/Second_domain/2'>second domain</scene> (residues 113-230) contains seven alpha helices that create a hydrophobic core.<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> The third domain (resudues 231-282) is the <scene name='56/566536/C-terminal/1'>C-Terminal</scene> domain that contains a bundle of three alpha helices. <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>

AlkA is composed of three main domains with dimensions of approximately 50 Angstroms, 45 Angstroms, and 25 Angstroms.<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> The first domain (residues 1-112) is the <scene name='56/566536/N_terminal_domain_and_dna/2'>N-terminal domain</scene> that is composed of a five stranded antiparallel beta sheet and two alpha helices.<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> The <scene name='56/566536/Second_domain/2'>second domain</scene> (residues 113-230) contains seven alpha helices that create a hydrophobic core.<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> The third domain (resudues 231-282) is the <scene name='56/566536/C-terminal/1'>C-Terminal</scene> domain that contains a bundle of three alpha helices. <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>

AlkA is a member of the helix-hairpin-helix (HhH) family of DNA glycosylases, where two compact alpha helical structures are connected by a hairpin loop.<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> In AlkA, the <scene name='56/566536/Hhh_domain/2'>HhH</scene> domain is composed of residues 202-227 and is responsible for binding the damaged DNA by van der Waals interactions, a few hydrogen bonds, and metal ion interactions.

@@ Line 12: / Line 12: @@
 ==Key Structures==
-AlkA is composed of three main domains with dimensions of approximately 50 Angstroms, 45 Angstroms, and 25 Angstroms.<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> The first domain (residues 1-112) is the <scene name='56/566536/N_terminal_domain_and_dna/1'>N-terminal domain</scene> that is composed of a five stranded antiparallel beta sheet and two alpha helices.<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> The <scene name='56/566536/Second_domain/2'>second domain</scene> (residues 113-230) contains seven alpha helices that create a hydrophobic core.<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> The third domain (resudues 231-282) is the <scene name='56/566536/C-terminal/1'>C-Terminal</scene> domain that contains a bundle of three alpha helices. <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>
+AlkA is composed of three main domains with dimensions of approximately 50 Angstroms, 45 Angstroms, and 25 Angstroms.<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> The first domain (residues 1-112) is the <scene name='56/566536/N_terminal_domain_and_dna/2'>N-terminal domain</scene> that is composed of a five stranded antiparallel beta sheet and two alpha helices.<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> The <scene name='56/566536/Second_domain/2'>second domain</scene> (residues 113-230) contains seven alpha helices that create a hydrophobic core.<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> The third domain (resudues 231-282) is the <scene name='56/566536/C-terminal/1'>C-Terminal</scene> domain that contains a bundle of three alpha helices. <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>
 AlkA is a member of the helix-hairpin-helix (HhH) family of DNA glycosylases, where two  compact alpha helical structures are connected by a hairpin loop.<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>  In AlkA, the <scene name='56/566536/Hhh_domain/2'>HhH</scene> domain is composed of residues 202-227 and is responsible for binding the damaged DNA by van der Waals interactions, a few hydrogen bonds, and metal ion interactions.