145d

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(New page: 200px<br /><applet load="145d" size="450" color="white" frame="true" align="right" spinBox="true" caption="145d, resolution 1.250&Aring;" /> '''STRUCTURE AND THERM...)
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[[Image:145d.gif|left|200px]]<br /><applet load="145d" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="145d, resolution 1.250&Aring;" />
 
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'''STRUCTURE AND THERMODYNAMICS OF NONALTERNATING C/G BASE PAIRS IN Z-DNA: THE 1.3 ANGSTROMS CRYSTAL STRUCTURE OF THE ASYMMETRIC HEXANUCLEOTIDE D(M(5)CGGGM(5) CG)/D(M(5)CGCCM(5)CG)'''<br />
 
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==Overview==
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==Structure and thermodynamics of nonalternating C/G base pairs in Z-DNA: the 1.3 angstroms crystal structure of the asymmetric hexanucleotide D(M(5)CGGGM(5) CG)/D(M(5)CGCCM(5)CG)==
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We have solved the single-crystal X-ray structure of the complementary, hexanucleotides d(m5-CGGGm5CG) and d(m5CGCCm5CG). The hexamer duplex was, crystallized as Z-DNA, but contains a single C.G base pair that does not, follow the alternating pyrimidine/purine rule for Z-DNA formation. This is, the first crystal structure which serves to illustrate the structural, consequences of placing a cytosine in the sterically disfavored syn, conformation. In addition, since these sequences are not, self-complementary, the individual strands of this asymmetric hexamer are, unique in sequence and therefore distinguishable in the crystal lattice., Nevertheless, the crystal of this duplex is isomorphous with other Z-DNA, hexamer structures. The asymmetry of this hexamer sequence required that, the structure be solved using two unique models, which are distinguished, by the orientation of hexanucleotides in the crystal lattice. In one model, (the GG model) the cytosine in the syn conformation is packed against the, terminal guanine base of a symmetry-related hexamer, while in the, alternative model (the CC model) this cytosine sits exposed in a solvent, channel of the lattice. We find that neither model alone can completely, account for the observed electron densities. The two models ultimately, were refined together. A composite structure consisting of 65% GG model, and 35% CC model refined to an R-factor of 19.3%, which was significantly, lower than refinements using either model alone. A detailed analysis of, these two structures shows that, in spite of the out-of-alternation C.G, base pair, the features characteristic of Z-DNA have been maintained. Both, models, however, show significant local structural adjustments to, accommodate the single cytosine base which is forced to adopt the syn, conformation in each hexamer. In general, it appears that in order to, relieve the energetically unfavorable steric contacts between the cytosine, base in the syn conformation and the deoxyribose sugar, the base is forced, into a highly buckled conformation, and that this large buckle in turn, alters the conformation of neighboring residues. This unusual conformation, also significantly weakens base-stacking interactions between the cytosine, in syn and the adjacent residues in the helix and affects the exposure of, the bases to solvent. We conclude that this crystal structure provides a, molecular rationale for why nonalternating bases are energetically, disfavored in Z-DNA.
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<StructureSection load='145d' size='340' side='right'caption='[[145d]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[145d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=145D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=145D FirstGlance]. <br>
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145D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=145D OCA].
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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]] 1.25&#8491;</td></tr>
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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>, <scene name='pdbligand=MCY:5-METHYL-2-DEOXYCYTIDINE'>MCY</scene></td></tr>
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==Reference==
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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=145d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=145d OCA], [https://pdbe.org/145d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=145d RCSB], [https://www.ebi.ac.uk/pdbsum/145d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=145d ProSAT]</span></td></tr>
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Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG)., Schroth GP, Kagawa TF, Ho PS, Biochemistry. 1993 Dec 14;32(49):13381-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8257675 8257675]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Ho, P.Shing.]]
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</StructureSection>
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[[Category: Kagawa, T.F.]]
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[[Category: Large Structures]]
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[[Category: Schroth, G.P.]]
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[[Category: Kagawa TF]]
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[[Category: double helix]]
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[[Category: Schroth GP]]
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[[Category: modified]]
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[[Category: Shing Ho P]]
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[[Category: z-dna]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:56:03 2007''
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Current revision

Structure and thermodynamics of nonalternating C/G base pairs in Z-DNA: the 1.3 angstroms crystal structure of the asymmetric hexanucleotide D(M(5)CGGGM(5) CG)/D(M(5)CGCCM(5)CG)

PDB ID 145d

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