3BSE

Crystal structure analysis of a 16-base-pair B-DNA

3BSE の概要

• エントリーDOI: 10.2210/pdb3bse/pdb
• 分子名称: DNA (5'-D(*DA*DCP*DAP*DCP*DTP*DAP*DCP*DAP*DAP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DAP*DT)-3'), DNA (5'-D(*DG*DTP*DAP*DTP*DTP*DGP*DCP*DAP*DAP*DCP*DAP*DTP*DTP*DGP*DTP*DAP*DGP*DT)-3'), CALCIUM ION, ... (4 entities in total)
• 機能のキーワード: dm domain, dna structure, doublesex, protein-dna recognition, sex determination, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 11510.14

構造登録者

Narayana, N. (登録日: 2007-12-23, 公開日: 2008-12-23, 最終更新日: 2024-02-21)

主引用文献

Narayana, N.,Weiss, M.A.
Crystallographic Analysis of a Sex-Specific Enhancer Element: Sequence-Dependent DNA Structure, Hydration, and Dynamics
J.Mol.Biol., 385:469-490, 2009

PubMed Abstract: The crystal structure of a sex-specific enhancer element is described at a resolution of 1.6 A. This 16-bp site, designated Dsx(A), functions in the regulation of a genetic switch between male and female patterns of gene expression in Drosophila melanogaster. Related sites are broadly conserved in metazoans, including in the human genome. This enhancer element is unusually rich in general regulatory sequences related to DNA recognition by multiple classes of eukaryotic transcription factors, including the DM motifs, homeodomain, and high mobility group box. Whereas free DNA is often crystallized as an A-form double helix, Dsx(A) was crystallized as B-DNA and thus provides a model for the prebound conformation of diverse regulatory DNA complexes. Sequence-dependent conformational properties that extend features of shorter B-DNA fragments with respect to double helical parameters, groove widths, hydration, and binding of divalent metal ions are observed. The structure also exhibits a sequence-dependent pattern of isotropic thermal B-factors, suggesting possible variation in the local flexibility of the DNA backbone. Such fluctuations are in accord with structural variability observed in prior B-DNA structures. We speculate that sites of intrinsic flexibility within a DNA control element provide hinges for its protein-directed reorganization in a transcriptional preinitiation complex.

PubMed: 18992257
DOI: 10.1016/j.jmb.2008.10.041

実験手法

X-RAY DIFFRACTION (1.6 Å)