|
|
| (13 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| [[Image:1cvy.gif|left|200px]]<br /><applet load="1cvy" size="450" color="white" frame="true" align="right" spinBox="true"
| |
| caption="1cvy, resolution 2.15Å" />
| |
| '''CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG'''<br />
| |
|
| |
|
| ==Overview== | | ==CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO 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='1cvy' size='340' side='right'caption='[[1cvy]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1cvy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CVY FirstGlance]. <br> |
| 1CVY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with IPY as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CVY 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]] 2.15Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPY:IMIDAZOLE-PYRROLE+POLYAMIDE'>IPY</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=1cvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvy OCA], [https://pdbe.org/1cvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cvy RCSB], [https://www.ebi.ac.uk/pdbsum/1cvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cvy 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: IPY]] | | [[Category: Rees DC]] |
| [[Category: double drug in minor groove]] | | [[Category: White S]] |
| [[Category: imidazole-pyrrole polyamide]] | |
| [[Category: minor groove recognition]] | |
| | |
| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:01:04 2007''
| |
