1cvx
From Proteopedia
(New page: 200px<br /><applet load="1cvx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1cvx, resolution 2.27Å" /> '''CRYSTAL STRUCTURE OF...) |
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| - | [[Image:1cvx.gif|left|200px]]<br /><applet load="1cvx" size=" | + | [[Image:1cvx.gif|left|200px]]<br /><applet load="1cvx" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1cvx, resolution 2.27Å" /> | caption="1cvx, resolution 2.27Å" /> | ||
'''CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG'''<br /> | '''CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole | + | Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference. |
==About this Structure== | ==About this Structure== | ||
| - | 1CVX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with HP2 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1CVX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=HP2:'>HP2</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVX OCA]. |
==Reference== | ==Reference== | ||
Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove., Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC, J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10623546 10623546] | Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove., Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC, J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10623546 10623546] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Baird, E | + | [[Category: Baird, E E.]] |
| - | [[Category: Bremer, R | + | [[Category: Bremer, R E.]] |
| - | [[Category: Dervan, P | + | [[Category: Dervan, P B.]] |
| - | [[Category: Kielkopf, C | + | [[Category: Kielkopf, C L.]] |
| - | [[Category: Rees, D | + | [[Category: Rees, D C.]] |
[[Category: White, S.]] | [[Category: White, S.]] | ||
[[Category: HP2]] | [[Category: HP2]] | ||
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[[Category: ta recognition]] | [[Category: ta recognition]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:10:16 2008'' |
Revision as of 10:10, 21 February 2008
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CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG
Overview
Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.
About this Structure
1CVX is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove., Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC, J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:10623546
Page seeded by OCA on Thu Feb 21 12:10:16 2008
