P53-DNA Recognition: Difference between revisions
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==Hoogsteen vs. Watson-Crick Base Pair in p53 Binding Sites== | ==Hoogsteen vs. Watson-Crick Base Pair in p53 Binding Sites== | ||
The distinct <scene name='Sandbox_Reserved_170/Arg248/2'>shape of the minor groove recognized by Arg248</scene> is due to a transition of the four A/T base pairs of the CATG core elements to a Hoogsteen base pairing geometry. Regions with Hoogsteen base pairs | The distinct <scene name='Sandbox_Reserved_170/Arg248/2'>shape of the minor groove recognized by Arg248</scene> is due to a transition of the four A/T base pairs of the CATG core elements to a Hoogsteen base pairing geometry. Regions with <font color='#00e000'>'''Hoogsteen base pairs</font> <scene name='Sandbox_Reserved_170/Hg_helix/2'>decrease the diameter of the double helix</scene> compared to regions with <font color='#2020ff'>'''Watson-Crick base pairs'''</font>. | ||
The reason for this deformation of the double helix is the <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>base pairing geometry in Hoogsteen base pairs</scene> with the approximately 180 degree rotation of adenine around the glycosidic bond and formation of hydrogen bonds with thymine at a different edge of the adenine base compared to <scene name='Group:USC-LCHS/3kmd_wcbp_closeup/1'>standard Watson-Crick base pairing</scene>, depicted here for the identical base pair in a p53 response element with different sequence from [[3kmd|PDB ID# 3KMD]]. | The reason for this deformation of the double helix is the <scene name='Group:USC-LCHS/3kz8_ba_hoogsteencloseup/2'>base pairing geometry in Hoogsteen base pairs</scene> with the approximately 180 degree rotation of adenine around the glycosidic bond and formation of hydrogen bonds with thymine at a different edge of the adenine base compared to <scene name='Group:USC-LCHS/3kmd_wcbp_closeup/1'>standard Watson-Crick base pairing</scene>, depicted here for the identical base pair in a p53 response element with different sequence from [[3kmd|PDB ID# 3KMD]]. | ||