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M103097200v1
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Papers In Press, published online ahead of print July 3, 2001
J. Biol. Chem, 10.1074/jbc.M103097200
Submitted on April 9, 2001
Revised on June 21, 2001
Accepted on July 2, 2001

Altering the DNA-binding specificity of the yeast matalpha2 homeodomain protein

Jonathan R. Mathias, Hualin Zhong, Yisheng Jin, and Andrew K. Vershon

Molecular Biology and Biochemistry, Waksman Institute, Rutgers University, Piscatatway, NJ 08854-8020

Corresponding Author: vershon{at}waksman.rutgers.edu

Homeodomain proteins are a highly conserved class of DNA-binding proteins that are found in virtually every eukaryotic organism. The conserved mechanism that these proteins use to bind DNA suggests that there may be at least a partial DNA recognition code for this class of proteins. To test this idea, we have investigated the sequence-specific requirements for DNA binding and repression by the yeast alpha 2 homeodomain protein in association with its co-factors, Mcm1 and a1. We have determined the contribution for each residue in the alpha 2 homeodomain that contacts the DNA in the co-crystal structures of the protein. We have also engineered mutants in the alpha 2 homeodomain to alter the DNA-binding specificity of the protein. While we were unable to change the specificity of alpha 2 by making substitutions at residues 47, 54 and 55, we have been able to alter the DNA-binding specificity by making substitutions at residue 50 of the homeodomain. Since other homeodomain proteins show similar changes in specificity with substitutions at residue 50, this suggests that there is at least a partial DNA recognition code at this position.


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