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327d

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[[Image:327d.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)==
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|PDB= 327d |SIZE=350|CAPTION= <scene name='initialview01'>327d</scene>, resolution 1.940&Aring;
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<StructureSection load='327d' size='340' side='right'caption='[[327d]], [[Resolution|resolution]] 1.94&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'>[[327d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=327D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=327D 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]] 1.94&#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=327d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=327d OCA], [https://pdbe.org/327d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=327d RCSB], [https://www.ebi.ac.uk/pdbsum/327d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=327d ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)'''
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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: Ramakrishnan B]]
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It is well known that methylation of alternating Py x Pu sequences potentiates the formation of Z-DNA. However, we have now observed that methylation of the alternating Z-DNA oligomer d(GCGCGCGCGC), which starts with a 5'-purine, unexpectedly stabilizes the A-DNA conformation. The double methyl derivative d(Gm5CGm5CGCGCGC), which crystallizes as duplex A-DNA in the hexagonal space group P6(1)22, a = b = 39.33 A and c = 77.93 A with one strand per asymmetric unit and six duplexes in the unit cell, refined to an R factor of 19.1 for 204 DNA atoms and 43 solvent molecules. This is the first report of a DNA sequence crystallized in both right and left-handed conformations, allowing structural comparisons not previously possible and, more importantly, this is the first time that methylation has been shown to potentiate the formation of A-DNA from a sequence known to crystallize as Z-DNA. From this study, ten base-pairs appear to be the critical length in determining the handedness of d(GC)n-type sequences in the crystalline state. Because methylation of nuclear DNA is linked to a number of cellular processes, including transcriptional inactivation, this study has important implications for the role of A-DNA in methylated regions of genomic DNA and, thus, in the regulation of gene expression. In this context, the structure of d(Gm5Cm5CGCGCGC) will be compared with that of the alternating A-DNA decamer d(GCACGCGTGC) and the alternating Z-DNA decamer d(GCGCGCGCGC) and discussed in terms of the forces that govern the handedness of duplex DNA oligomers.
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[[Category: Sundaralingam M]]
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[[Category: Tippin DB]]
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==About this Structure==
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327D 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=327D OCA].
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==Reference==
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Methylation of the Z-DNA decamer d(GC)5 potentiates the formation of A-DNA: crystal structure of d(Gm5CGm5CGCGCGC)., Tippin DB, Ramakrishnan B, Sundaralingam M, J Mol Biol. 1997 Jul 11;270(2):247-58. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9236126 9236126]
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[[Category: Protein complex]]
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[[Category: Ramakrishnan, B.]]
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[[Category: Sundaralingam, M.]]
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[[Category: Tippin, D B.]]
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[[Category: a-dna]]
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[[Category: double helix]]
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[[Category: modified]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:54:37 2008''
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Current revision

CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)

PDB ID 327d

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