1ue2: Difference between revisions
New page: left|200px<br /><applet load="1ue2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ue2, resolution 1.4Å" /> '''Crystal structure of ... |
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[[Image:1ue2.gif|left|200px]]<br /><applet load="1ue2" size=" | [[Image:1ue2.gif|left|200px]]<br /><applet load="1ue2" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1ue2, resolution 1.4Å" /> | caption="1ue2, resolution 1.4Å" /> | ||
'''Crystal structure of d(GI5CGAAAGCT)'''<br /> | '''Crystal structure of d(GI5CGAAAGCT)'''<br /> | ||
==Overview== | ==Overview== | ||
A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin | A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson-Crick G.C base pairs and a subsequent sheared G.A pair at both ends. The central two A residues are free from base-pair formation. The corresponding base moieties of the two strands are intercalated and stacked on each other, forming a long column of G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*) (asterisks indicate the counter-strand). The Watson-Crick and major-groove sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to those found in the nonamers d(G(Br)CGAAAGCT) and d(G(I)CGAAAGCT), the base-intercalated duplex may be a stable form of the specific sequence. Electrophoresis results suggest that the octamer has two states, monomeric and dimeric, in solution depending on the Mg(2+) concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions. | ||
==About this Structure== | ==About this Structure== | ||
1UE2 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CL, MG and NCO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | 1UE2 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UE2 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: zipper-like duplex]] | [[Category: zipper-like duplex]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:23:31 2008'' | ||
Revision as of 13:23, 21 February 2008
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Crystal structure of d(GI5CGAAAGCT)
Overview
A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson-Crick G.C base pairs and a subsequent sheared G.A pair at both ends. The central two A residues are free from base-pair formation. The corresponding base moieties of the two strands are intercalated and stacked on each other, forming a long column of G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*) (asterisks indicate the counter-strand). The Watson-Crick and major-groove sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to those found in the nonamers d(G(Br)CGAAAGCT) and d(G(I)CGAAAGCT), the base-intercalated duplex may be a stable form of the specific sequence. Electrophoresis results suggest that the octamer has two states, monomeric and dimeric, in solution depending on the Mg(2+) concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions.
About this Structure
1UE2 is a Protein complex structure of sequences from [1] with CL, MG and NCO as ligands. Full crystallographic information is available from OCA.
Reference
Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure., Sunami T, Kondo J, Hirao I, Watanabe K, Miura KI, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):90-6. Epub 2003 Dec, 18. PMID:14684897
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