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Nucleic Acids Research 2005 33(1):430-438; doi:10.1093/nar/gki191
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Published online 14 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 00 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.

Article

Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d

Chin-Yu Chen1,3, Tzu-Ping Ko1, Ting-Wan Lin1, Chia-Cheng Chou1,2, Chun-Jung Chen4 and Andrew H.-J. Wang1,2,*

1 Institute of Biological Chemistry Taipei 115, Taiwan 2 Core Facility for Protein X-ray Crystallography, Academia Sinica Taipei 115, Taiwan 3 Department of Chemistry, National Taiwan University Taipei 106, Taiwan 4 Biology Group, National Synchrotron Radiation Research Center Hsinchu 30077, Taiwan

*To whom correspondence should be addressed at Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan. Tel: +886 2 2788 1918; Fax: +886 2 2788 2043; Email: ahjwang{at}gate.sinica.edu.tw

Received September 14, 2004. Revised December 10, 2004. Accepted December 23, 2004.

Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (~60°) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant–DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (~50°). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (~80°). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower T m values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA.


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