206d | pdb_0000206d
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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 SPM 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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