User:Andrea Foote/Sandbox 1: Difference between revisions

Line 11:

The domains of Purα have been described as "Whirly-like" folds because of their structural similarity to the DNA-binding Whirly class of proteins found in plants.<ref>PMID:19846792</ref> Whirlys are also ssDNA binding proteins, however unlike Purα they are not sequence-specific.

The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues involved in protein-DNA conjugation are: <scene name='78/786627/Repeati_resi/1'>(repeat I) Q52, S53 and K54</scene>; (repeat II) K138, N140, R142, and F145. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 (repeat II) of the protein. This phenylalanine-guanine stacking interaction disrupts base-stacking within the DNA resulting in the following cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity.<ref>PMID:26744780</ref>

The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues involved in protein-DNA conjugation are: <scene name='78/786627/Repeati_resi/2'>(repeat I) Q52, S53 and K54</scene>; (repeat II) K138, N140, R142, and F145. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 (repeat II) of the protein. This phenylalanine-guanine stacking interaction disrupts base-stacking within the DNA resulting in the following cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity.<ref>PMID:26744780</ref>

== Function ==

@@ Line 11: / Line 11: @@
 The domains of Purα have been described as "Whirly-like" folds because of their structural similarity to the DNA-binding Whirly class of proteins found in plants.<ref>PMID:19846792</ref> Whirlys are also ssDNA binding proteins, however unlike Purα they are not sequence-specific.
-The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues involved in protein-DNA conjugation are: <scene name='78/786627/Repeati_resi/1'>(repeat I) Q52, S53 and K54</scene>; (repeat II) K138, N140, R142, and F145. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 (repeat II) of the protein. This phenylalanine-guanine stacking interaction disrupts base-stacking within the DNA resulting in the following cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity.<ref>PMID:26744780</ref>
+The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues involved in protein-DNA conjugation are: <scene name='78/786627/Repeati_resi/2'>(repeat I) Q52, S53 and K54</scene>; (repeat II) K138, N140, R142, and F145. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 (repeat II) of the protein. This phenylalanine-guanine stacking interaction disrupts base-stacking within the DNA resulting in the following cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity.<ref>PMID:26744780</ref>
 == Function ==