1d31: Difference between revisions
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[[Image:1d31.jpg|left|200px]] | [[Image:1d31.jpg|left|200px]] | ||
'''THE THREE-DIMENSIONAL STRUCTURES OF BULGE-CONTAINING DNA FRAGMENTS''' | {{Structure | ||
|PDB= 1d31 |SIZE=350|CAPTION= <scene name='initialview01'>1d31</scene>, resolution 2.600Å | |||
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|LIGAND= | |||
|ACTIVITY= | |||
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'''THE THREE-DIMENSIONAL STRUCTURES OF BULGE-CONTAINING DNA FRAGMENTS''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1D31 is a [ | 1D31 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=1D31 OCA]. | ||
==Reference== | ==Reference== | ||
Three-dimensional structures of bulge-containing DNA fragments., Joshua-Tor L, Frolow F, Appella E, Hope H, Rabinovich D, Sussman JL, J Mol Biol. 1992 May 20;225(2):397-431. PMID:[http:// | Three-dimensional structures of bulge-containing DNA fragments., Joshua-Tor L, Frolow F, Appella E, Hope H, Rabinovich D, Sussman JL, J Mol Biol. 1992 May 20;225(2):397-431. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1593627 1593627] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Appella, E.]] | [[Category: Appella, E.]] | ||
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[[Category: Sussman, J L.]] | [[Category: Sussman, J L.]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: | [[Category: bulge]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: flipped-out base]] | [[Category: flipped-out base]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:32:10 2008'' | ||
Revision as of 11:32, 20 March 2008
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THE THREE-DIMENSIONAL STRUCTURES OF BULGE-CONTAINING DNA FRAGMENTS
OverviewOverview
The three-dimensional structure of a DNA tridecamer d(CGCAGAATTCGCG)2 containing bulged adenine bases was determined by single crystal X-ray diffraction methods, at 120 K, to 2.6 A resolution. The structure is a B-DNA type double helix with a single duplex in the asymmetric unit. One of the bulged adenine bases loops out from the double helix, while the other stacks in to it. This is in contrast to our preliminary finding, which indicated that both adenine bases were looped out. This revised model was confirmed by the use of a covalently bound heavy-atom derivative. The conformation of the looped-out bulge hardly disrupts base stacking interactions of the bases flanking it. This is achieved by the backbone making a "loop-the-loop" curve with the extra adenine flipping over with respect to the other nucleotides in the strand. The looped-out base intercalates into the stacked-in bulge site of a symmetrically related duplex. The looped-out and stacked-in bases form an A.A reversed Hoogsteen base-pair that stacks between the surrounding base-pairs, thus stabilizing both bulges. The double helix is frayed at one end with the two "melted" bases participating in intermolecular interactions. A related structure, of the same tridecamer, after soaking the crystals with proflavin, was determined to 3.2 A resolution. The main features of this B-DNA duplex are basically similar to the native tridecamer but differ in detail especially in the conformation of the bulged-out base. Accommodation of a large perturbation such as that described here with minimal disruption of the double helix shows both the flexibility and resiliency of the DNA molecule.
About this StructureAbout this Structure
1D31 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Three-dimensional structures of bulge-containing DNA fragments., Joshua-Tor L, Frolow F, Appella E, Hope H, Rabinovich D, Sussman JL, J Mol Biol. 1992 May 20;225(2):397-431. PMID:1593627
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