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Nucleic Acids Research, 1995, Vol. 23, No. 11 2065-2073
© 1995

STRUCTURAL BIOLOGY

Base-pair opening and spermine binding—B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition

Leslie W. Tari and Anthony S. Secco*

Department of Chemistry, University of Manitoba Winnipeg, Manitoba R3T 2N2, Canada

* To whom correspondence should be addressed

Received August 24, 1994. Revised April 15, 1995. Accepted April 17, 1995.

A sequence that is represented frequently in functionally important sites Involving proteln-DNA interactions is GTG/CAC, suggesting that the trimer may play a role in regulatory processes. The 2.5 Å resolution structure of d(CGGTGG)/d(CCACCG), a part of the Interior operator (O1,, 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 crystallographlc asymmetric unit. The hexamer exhibits base-pair opening and shearing at TA 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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