2HOT

Phage selected homeodomain bound to modified DNA

Summary for 2HOT

• Entry DOI: 10.2210/pdb2hot/pdb
• Related: 2HDD 2HOS
• Descriptor: 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*CP*CP*GP*GP*A)-3', 5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3', Segmentation polarity homeobox protein engrailed, ... (6 entities in total)
• Functional Keywords: homeodomain, phage display, transcription-dna complex, transcription/dna
• Biological source: Drosophila melanogaster (fruit fly); More
• Cellular location: Nucleus : P02836
• Total number of polymer chains: 4
• Total formula weight: 28227.71

Authors

Feldman, M.E.,Simon, M.D.,Shokat, K.M. (deposition date: 2006-07-16, release date: 2006-12-12, Last modification date: 2024-02-14)

Primary citation

Simon, M.D.,Feldman, M.E.,Rauh, D.,Maris, A.E.,Wemmer, D.E.,Shokat, K.M.
Structure and properties of a re-engineered homeodomain protein-DNA interface.
Acs Chem.Biol., 1:755-760, 2006

PubMed Abstract: The homeodomain (HD)-DNA interface has been conserved over 500 million years of evolution. Despite this conservation, we have successfully re-engineered the engrailed HD to specifically recognize an unnatural nucleotide using a phage display selection. Here we report the synthesis of novel nucleosides and the selection of mutant HDs that bind these nucleotides using phage display. The high-resolution crystal structure of one mutant in complex with modified and unmodified DNA demonstrates that, even with the substantial perturbation to the interface, this selected mutant retains a canonical HD structure. Dissection of the contributions due to each of the selected mutations reveals that the majority of the modification-specific binding is accomplished by a single mutation (I47G) but that the remaining mutations retune the stability of the HD. These results afford a detailed look at a re-engineered protein-DNA interaction and provide insight into the opportunities for re-engineering highly conserved interfaces.

PubMed: 17240973
DOI: 10.1021/cb6003756

Experimental method

X-RAY DIFFRACTION (2.19 Å)