Nucleic Acids Research, 2000, Vol. 28, No. 20 3853-3863
© 2000 Oxford University Press
Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation
The Wistar Institute and The Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
HAP1 is a transcription factor in yeast whose DNA-binding domain has been implicated in directly affecting transcriptional activation. Two separate mutations in the DNA-binding domain, S63G (HAP1-PC7) and S63R (HAP1-18), retain wild-type binding affinity. However, HAP1-PC7 is transcriptionally silent while HAP1-18 shows highly elevated levels of transcription. We have determined the X-ray crystal structure of the DNA-binding domain of HAP1-PC7 bound to its DNA target, UASCYC7, and compared it to the previously solved HAP1-wt and HAP1-18 complexes to UASCYC7. Additionally, we have quantitatively compared the DNA-binding affinity and specificity of the HAP1-PC7, HAP1-18 and HAP1-wt DNA-binding domains. We show that, although the DNA-binding domains of these three proteins bind UASCYC7 with comparable affinity and specificity, the protein–DNA interactions are dramatically different between the three complexes. Conserved protein–DNA interactions are largely restricted to an internal DNA sequence that excludes one of the two conserved DNA half-sites of UASCYC7 suggesting a mode of recognition distinct from other HAP1 family members. Alternative protein–DNA interactions result in divergent DNA configurations between the three complexes. These results suggest that the differential transcriptional activities of the HAP1, HAP1-18 and HAP1-PC7 proteins are due, at least in part, to alternative protein–DNA contacts, and implies that HAP1–DNA interactions have direct allosteric effects on transcriptional activation.
* To whom correspondence should be addressed. Tel: +1 215 898 5006; Fax: +1 215 898 0381; Email: marmor@wistar.upenn.edu Present address: Daniel A. King, Sarah Lawrence College, 1 Mead Way, Bronxville, NY 10708, USA The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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