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| | <StructureSection load='6j0h' size='340' side='right'caption='[[6j0h]], [[Resolution|resolution]] 1.52Å' scene=''> | | <StructureSection load='6j0h' size='340' side='right'caption='[[6j0h]], [[Resolution|resolution]] 1.52Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6j0h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J0H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6j0h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J0H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.52Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PXZ:2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE'>PXZ</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [http://pdbe.org/6j0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [http://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h 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=6j0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j0h OCA], [https://pdbe.org/6j0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j0h RCSB], [https://www.ebi.ac.uk/pdbsum/6j0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j0h ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hou, M H]] | + | [[Category: Streptomyces sp]] |
| - | [[Category: Satange, R B]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Actinomycin d]] | + | [[Category: Hou MH]] |
| - | [[Category: Base flip out]] | + | [[Category: Satange RB]] |
| - | [[Category: Dna kink]]
| + | |
| - | [[Category: Dna-antibiotic complex]]
| + | |
| - | [[Category: Drug-dna complex]]
| + | |
| - | [[Category: Mismatch dna]]
| + | |
| Structural highlights
6j0h is a 2 chain structure with sequence from Streptomyces sp. and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.52Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn-syn, water mediated anti-syn and syn-syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5' intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation.,Satange R, Chuang CY, Neidle S, Hou MH Nucleic Acids Res. 2019 Jul 30. pii: 5541096. doi: 10.1093/nar/gkz653. PMID:31361900[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Satange R, Chuang CY, Neidle S, Hou MH. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Res. 2019 Jul 30. pii: 5541096. doi: 10.1093/nar/gkz653. PMID:31361900 doi:http://dx.doi.org/10.1093/nar/gkz653
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