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A more recent version of this article appeared on January 3, 2003
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M207504200v1
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Papers In Press, published online ahead of print October 29, 2002
J. Biol. Chem, 10.1074/jbc.M207504200
Submitted on July 25, 2002
Revised on October 28, 2002
Accepted on October 29, 2002

Lock and key binding of the HOX YPWM peptide to the PBX homeodomain

Tara Sprules, Nancy Green, Mark Featherstone, and Kalle Gehring

Dept. of Chemistry, University of Alberta, Edmonton, AB T6G 2G2

Corresponding Author: tara.sprules{at}ualberta.ca

HOX homeodomain proteins bind short core DNA sequences to control very specific developmental processes. DNA binding affinity and sequence selectivity is increased by the formation of cooperative complexes with the PBX homeodomain protein. A conserved YPWM motif in the HOX protein is necessary for cooperative binding with PBX. We have determined the structure of a PBX homeodomain bound to a 14mer DNA duplex. A relaxation optimized procedure was developed to measure DNA residual dipolar couplings at natural abundance in the 20 kDa binary complex. When bound to DNA, a fourth alpha-helix forms in the PBX homeodomain. This helix rigidifies the DNA recognition helix of PBX and forms a hydrophobic binding site for the HOX YPXM peptide. The HOX peptide itself shows some structure in solution suggesting that the interaction between PBX and HOX is an example of “lock and key” binding. The NMR structure explains the requirement of DNA for the PBX-HOX interaction and the increased affinity of DNA binding.


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