SNAP output for PDB entry 2hot [SNAP web server]

PDB-id

2hot; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA

Method

X-ray (2.19 Å)

Summary

Phage selected homeodomain bound to modified DNA

Reference

Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE, Shokat KM (2006): "Structure and properties of a re-engineered homeodomain protein-DNA interface." Acs Chem.Biol., 1, 755-760. doi: 10.1021/cb6003756.

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.