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1f6i

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[[Image:1f6i.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGM5CC==
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|PDB= 1f6i |SIZE=350|CAPTION= <scene name='initialview01'>1f6i</scene>, resolution 2.2&Aring;
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<StructureSection load='1f6i' size='340' side='right'caption='[[1f6i]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1f6i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6I FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6i OCA], [https://pdbe.org/1f6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6i RCSB], [https://www.ebi.ac.uk/pdbsum/1f6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6i ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGM5CC'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Eichman BF]]
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Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3'-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway from B-DNA to A-DNA through the E-DNA intermediate in a single sequence. The E-DNA surface is highly accessible to solvent, with waters in the major groove sitting on exposed faces of the stacked nucleotides. We suggest that the geometry of the waters and the stacked base pairs would promote the spontaneous deamination of 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base pairs.
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[[Category: Ho PS]]
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[[Category: Vargason JM]]
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==About this Structure==
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1F6I is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6I OCA].
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==Reference==
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The extended and eccentric E-DNA structure induced by cytosine methylation or bromination., Vargason JM, Eichman BF, Ho PS, Nat Struct Biol. 2000 Sep;7(9):758-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10966645 10966645]
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[[Category: Protein complex]]
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[[Category: Eichman, B F.]]
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[[Category: Ho, P S.]]
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[[Category: Vargason, J M.]]
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[[Category: double helix]]
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[[Category: e-dna]]
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[[Category: methylation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:05:05 2008''
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Current revision

CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGM5CC

PDB ID 1f6i

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