Sandbox Reserved 829: Difference between revisions
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''* Helix 3'' | ''* Helix 3'' | ||
Helix 3 of PDX-1 forms specific interactions in the major groove with the bases Ade 2, Ade 3, and Thy 4 of the TAAT core of the DNA, and the bases Cyt 5*, Thy 6*, and Cyt 7* of the DNA complementary strand. | Helix 3 of PDX-1 forms specific interactions in the major groove with the bases Ade 2, Ade 3, and Thy 4 of the TAAT core of the DNA, and the bases Cyt 5*, Thy 6*, and Cyt 7* of the DNA complementary strand. | ||
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[[Image:Nter.jpg|left|500px|thumb|PDX-1 homedomain/DNA interactions | [[Image:Nter.jpg|left|500px|thumb|PDX-1 homedomain/DNA interactions. | ||
A | A) Structure of the PDX-1 homedomain/DNA complex. | ||
B | B) Hydrogen bond contacts with the DNA differ between Conformation A and B. | ||
<ref name= "binding" />]] | <ref name= "binding" />]] | ||
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''* The N-terminal arm '' | ''* The N-terminal arm '' | ||
The N-terminal arm (residues 1 to 9) of PDX-1 homeodomain, first contacts the core TAAT bases of the DNA through the minor groove and contributes to the binding specificity. In PDX-1, the N-terminal sequence contains three basic residues : Lys 2, Arg 3 and Arg 5. | The N-terminal arm (residues 1 to 9) of PDX-1 homeodomain, first contacts the core TAAT bases of the DNA through the minor groove and contributes to the binding specificity. In PDX-1, the N-terminal sequence contains three basic residues : Lys 2, Arg 3 and Arg 5. | ||
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So, the most stable configuration for the N-terminal arm of Pdx1 consists of Lys 2 inserted in the minor groove and Arg 3 outside of the minor grove contacting the phosphate backbone and Arg 43. | So, the most stable configuration for the N-terminal arm of Pdx1 consists of Lys 2 inserted in the minor groove and Arg 3 outside of the minor grove contacting the phosphate backbone and Arg 43. | ||
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''* The DNA curvature '' | ''* The DNA curvature '' | ||
Furthermore, the DNA curvature in conformation A or B differs from each other. The curvature of the DNA in conformation B is around 34° while the conformation A enable a curvature around 16°. | Furthermore, the DNA curvature in conformation A or B differs from each other. The curvature of the DNA in conformation B is around 34° while the conformation A enable a curvature around 16°. | ||
