206d

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(New page: 200px<br /><applet load="206d" size="350" color="white" frame="true" align="right" spinBox="true" caption="206d, resolution 2.500&Aring;" /> '''BASE-PAIR OPENING A...)
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==Overview==
==Overview==
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A sequence that is represented frequently in functionally important sites, involving protein-DNA interactions is GTG/CAC, suggesting that the trimer, may play a role in regulatory processes. The 2.5 A resolution structure of, d(CGGTGG)/d(CCACCG), a part of the interior operator (OI, nucleotides +44, to +49) of the gal operon, co-crystallized with spermine, is described, herein. The crystal packing arrangement in this structure is unprecedented, in a crystal of B-DNA, revealing a close packing of columns of stacked DNA, resembling a 5-stranded twisted wire cable. The final structure contains, one hexamer duplex, 17 water molecules and 1.5 spermine molecules per, crystallographic asymmetric unit. The hexamer exhibits base-pair opening, and shearing at T.A resulting in a novel non-Watson-Crick hydrogen-bonding, scheme between adenine and thymine in the GTG region. The ability of this, sequence to adopt unusual conformations in its GTG region may be a, critical factor conferring sequence selectivity on the binding of Gal, repressor. In addition, this is the first conclusive example of a crystal, structure of spermine with native B-DNA, providing insight into the, mechanics of polyamine-DNA binding, as well as possible explanations for, the biological action of spermine.
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A sequence that is represented frequently in functionally important sites involving protein-DNA interactions is GTG/CAC, suggesting that the trimer may play a role in regulatory processes. The 2.5 A resolution structure of d(CGGTGG)/d(CCACCG), a part of the interior operator (OI, nucleotides +44 to +49) of the gal operon, co-crystallized with spermine, is described herein. The crystal packing arrangement in this structure is unprecedented in a crystal of B-DNA, revealing a close packing of columns of stacked DNA resembling a 5-stranded twisted wire cable. The final structure contains one hexamer duplex, 17 water molecules and 1.5 spermine molecules per crystallographic asymmetric unit. The hexamer exhibits base-pair opening and shearing at T.A resulting in a novel non-Watson-Crick hydrogen-bonding scheme between adenine and thymine in the GTG region. The ability of this sequence to adopt unusual conformations in its GTG region may be a critical factor conferring sequence selectivity on the binding of Gal repressor. In addition, this is the first conclusive example of a crystal structure of spermine with native B-DNA, providing insight into the mechanics of polyamine-DNA binding, as well as possible explanations for the biological action of spermine.
==About this Structure==
==About this Structure==
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Base-pair opening and spermine binding--B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition., Tari LW, Secco AS, Nucleic Acids Res. 1995 Jun 11;23(11):2065-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7596838 7596838]
Base-pair opening and spermine binding--B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition., Tari LW, Secco AS, Nucleic Acids Res. 1995 Jun 11;23(11):2065-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7596838 7596838]
[[Category: Protein complex]]
[[Category: Protein complex]]
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[[Category: Secco, A.S.]]
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[[Category: Secco, A S.]]
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[[Category: Tari, L.W.]]
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[[Category: Tari, L W.]]
[[Category: SPM]]
[[Category: SPM]]
[[Category: b-dna]]
[[Category: b-dna]]
[[Category: double helix]]
[[Category: double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:46:59 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:20:50 2008''

Revision as of 14:20, 21 February 2008

Image:206d.gif

206d, resolution 2.500Å

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BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION

Overview

A sequence that is represented frequently in functionally important sites involving protein-DNA interactions is GTG/CAC, suggesting that the trimer may play a role in regulatory processes. The 2.5 A resolution structure of d(CGGTGG)/d(CCACCG), a part of the interior operator (OI, nucleotides +44 to +49) of the gal operon, co-crystallized with spermine, is described herein. The crystal packing arrangement in this structure is unprecedented in a crystal of B-DNA, revealing a close packing of columns of stacked DNA resembling a 5-stranded twisted wire cable. The final structure contains one hexamer duplex, 17 water molecules and 1.5 spermine molecules per crystallographic asymmetric unit. The hexamer exhibits base-pair opening and shearing at T.A resulting in a novel non-Watson-Crick hydrogen-bonding scheme between adenine and thymine in the GTG region. The ability of this sequence to adopt unusual conformations in its GTG region may be a critical factor conferring sequence selectivity on the binding of Gal repressor. In addition, this is the first conclusive example of a crystal structure of spermine with native B-DNA, providing insight into the mechanics of polyamine-DNA binding, as well as possible explanations for the biological action of spermine.

About this Structure

206D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

Reference

Base-pair opening and spermine binding--B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition., Tari LW, Secco AS, Nucleic Acids Res. 1995 Jun 11;23(11):2065-73. PMID:7596838

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