SNAP output for PDB entry 1du0 [SNAP web server]

PDB-id

1du0; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA

Method

X-ray (2.0 Å)

Summary

Engrailed homeodomain q50a variant DNA complex

Reference

Grant RA, Rould MA, Klemm JD, Pabo CO (2000): "Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A." Biochemistry, 39, 8187-8192. doi: 10.1021/bi000071a.

Abstract

We have determined the crystal structure of a complex containing the engrailed homeodomain Gln50 --> Ala variant (QA50) bound to the wild-type optimal DNA site (TAATTA) at 2.0 A resolution. Biochemical and genetic studies by other groups have suggested that residue 50 is an important determinant of differential DNA-binding specificity among homeodomains (distinguishing among various sites of the general form TAATNN). However, biochemical studies of the QA50 variant had revealed that it binds almost as tightly as the wild-type protein and with only modest changes in specificity. We have now determined the crystal structure of the QA50 variant to help understand the role of residue 50 in site-specific recognition. Our cocrystal structure shows some interesting changes in the water structure at the site of the substitution and shows some changes in the conformations of neighboring side chains. However, the structure, like the QA50 biochemical data, suggests that Gln50 plays a relatively modest role in determining the affinity and specificity of the engrailed homeodomain.