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Science 21 January 1994:
Vol. 263. no. 5145, pp. 348 - 355
DOI: 10.1126/science.8278807
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Articles

Science, Vol 263, Issue 5145, 348-355
Copyright © 1994 by American Association for the Advancement of Science

articles

Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions

JA Feng, RC Johnson, and RE Dickerson

Molecular Biology Institute, University of California, Los Angeles 90024.

The structure of the 52-amino acid DNA-binding domain of the prokaryotic Hin recombinase, complexed with a DNA recombination half-site, has been solved by x-ray crystallography at 2.3 angstrom resolution. The Hin domain consists of a three-alpha-helix bundle, with the carboxyl-terminal helix inserted into the major groove of DNA, and two flanking extended polypeptide chains that contact bases in the minor groove. The overall structure displays features resembling both a prototypical bacterial helix-turn-helix and the eukaryotic homeodomain, and in many respects is an intermediate between these two DNA-binding motifs. In addition, a new structural motif is seen: the six-amino acid carboxyl-terminal peptide of the Hin domain runs along the minor groove at the edge of the recombination site, with the peptide backbone facing the floor of the groove and side chains extending away toward the exterior. The x-ray structure provides an almost complete explanation for DNA mutant binding studies in the Hin system and for DNA specificity observed in the Hin-related family of DNA invertases.


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