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| | == Structural highlights == | | == Structural highlights == |
| | <table><tr><td colspan='2'>[[1dj6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJ6 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[1dj6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJ6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=104:N,N-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE'>104</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[292d|292d]], [[293d|293d]], [[336d|336d]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=104:N,N-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE'>104</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dj6 OCA], [https://pdbe.org/1dj6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dj6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dj6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dj6 ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dj6 OCA], [https://pdbe.org/1dj6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dj6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dj6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dj6 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| Line 22: |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hakoshima, T]] | + | [[Category: Hakoshima T]] |
| - | [[Category: Nakanishi, I]] | + | [[Category: Nakanishi I]] |
| - | [[Category: Ohishi, H]] | + | [[Category: Ohishi H]] |
| - | [[Category: Ohtsuchi, M]] | + | [[Category: Ohtsuchi M]] |
| - | [[Category: Rich, A]] | + | [[Category: Rich A]] |
| - | [[Category: Tomita, K i]] | + | [[Category: Tomita K-i]] |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Polyamine binding in minor groove of z-dna]]
| + | |
| - | [[Category: X-ray crystal structure]]
| + | |
| - | [[Category: Z-dna:polyamine complex]]
| + | |
| Structural highlights
Publication Abstract from PubMed
The crystal structure of a left-handed Z-DNA hexamer, d(CG)(3) in complex with a synthetic polyamine, N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine, NH(3)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(2)(+)-(CH(2))(2)-NH(3)(+) [PA(222)], has been determined by the X-ray diffraction method at 1.0 A resolution. In an orthorhombic crystal, the d(CG)(3) duplex binds two PA(222) molecules, and this synthetic polyamine exhibits dual conformational properties. One of the two PA(222) molecules resides on the floor of the minor groove of a Z-DNA duplex and imino groups bridge the two phosphate chains across a double helix, while the terminal amino groups link the oxygen atoms O2 of four cytosine bases. This PA(222) molecule makes a U-turn like a fishhook at one of its ends to provide a micro-environmental network previously unseen in complexes of DNA with polyamines. The width of the minor groove does not become considerably greater with the looped end of the polyamine, indicating conformational rigidity of the Z-DNA backbone imposed by the high stacking energy of the GC base pairs. While polyamine binding to the minor groove has been postulated by theoretical studies for stabilizing the Z-DNA double helical conformation, the finding in the crystal of the looped polyamine chain binding the minor groove of Z-DNA is observed for the first time from the data collected at 10 degrees C (so-called room temperature data). Another PA(222) molecule binds on the convex outer surface of the major groove of the Z-DNA duplex and links three d(CG)(3) duplexes which are symmetrically related to each other. The structure of this PA(222) presents the previously reported zig-zag type conformation [Egli et al., Biochemistry 30 (1991) 11388-11402]. Comparison of this structure with other polyamine-DNA cocrystals reveals structural themes and differences that may relate to the length of the polyamine.
The crystal structure of N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine (polyamines) binding to the minor groove of d(CGCGCG)(2), hexamer at room temperature.,Ohishi H, Suzuki K, Ohtsuchi M, Hakoshima T, Rich A FEBS Lett. 2002 Jul 17;523(1-3):29-34. PMID:12123799[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ohishi H, Suzuki K, Ohtsuchi M, Hakoshima T, Rich A. The crystal structure of N(1)-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine (polyamines) binding to the minor groove of d(CGCGCG)(2), hexamer at room temperature. FEBS Lett. 2002 Jul 17;523(1-3):29-34. PMID:12123799
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