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| [[Image:1cvx.gif|left|200px]]<br /><applet load="1cvx" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1cvx, resolution 2.27Å" />
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| '''CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG'''<br />
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| ==Overview== | | ==CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG== |
| 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.
| | <StructureSection load='1cvx' size='340' side='right'caption='[[1cvx]], [[Resolution|resolution]] 2.27Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1cvx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CVX FirstGlance]. <br> |
| 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].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.27Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HP2:HYDROXYPYRROLE-IMIDAZOLE-PYRROLE+POLYAMIDE'>HP2</scene></td></tr> |
| ==Reference==
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvx OCA], [https://pdbe.org/1cvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cvx RCSB], [https://www.ebi.ac.uk/pdbsum/1cvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cvx ProSAT]</span></td></tr> |
| 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]
| | </table> |
| [[Category: Protein complex]] | | __TOC__ |
| [[Category: Baird, E E.]] | | </StructureSection> |
| [[Category: Bremer, R E.]] | | [[Category: Large Structures]] |
| [[Category: Dervan, P B.]] | | [[Category: Baird EE]] |
| [[Category: Kielkopf, C L.]] | | [[Category: Bremer RE]] |
| [[Category: Rees, D C.]] | | [[Category: Dervan PB]] |
| [[Category: White, S.]] | | [[Category: Kielkopf CL]] |
| [[Category: HP2]]
| | [[Category: Rees DC]] |
| [[Category: double drug in minor groove]]
| | [[Category: White S]] |
| [[Category: minor groove recognition]]
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| [[Category: polyamide]]
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| [[Category: ta recognition]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:10:16 2008''
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