2hdd
From Proteopedia
|
ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX
Overview
BACKGROUND: The homeodomain is one of the key DNA-binding motifs used in, eukaryotic gene regulation, and homeodomain proteins play critical roles, in development. The residue at position 50 of many homeodomains appears to, determine the differential DNA-binding specificity, helping to distinguish, among binding sites of the form TAATNN. However, the precise role(s) of, residue 50 in the differential recognition of alternative sites has not, been clear. None of the previously determined structures of, homeodomain-DNA complexes has shown evidence for a stable hydrogen bond, between residue 50 and a base, and there has been much discussion, based, in part on NMR studies, about the potential importance of water-mediated, contacts. This study was initiated to help clarify some of these issues., RESULTS: The crystal structure of a complex containing the engrailed, Gln50-->Lys variant (QK50) with its optimal binding site TAATCC (versus, TAATTA for the wild-type protein) has been determined at 1.9 A resolution., The overall structure of the QK50 variant is very similar to that of the, wild-type complex, but the sidechain of Lys50 projects directly into the, major groove and makes several hydrogen bonds to the O6 and N7 atoms of, the guanines at base pairs 5 and 6. Lys50 also makes an additional, water-mediated contact with the guanine at base pair 5 and has an, alternative conformation that allows a hydrogen bond with the O4 of the, thymine at base pair 4. CONCLUSIONS: The structural context provided by, the folding and docking of the engrailed homeodomain allows Lys50 to make, remarkably favorable contacts with the guanines at base pairs 5 and 6 of, the binding site. Although many different residues occur at position 50 in, different homeodomains, and although numerous position 50 variants have, been constructed, the most striking examples of altered specificity, usually involve introducing or removing a lysine sidechain from position, 50. This high-resolution structure also confirms the critical role of, Asn51 in homeodomain-DNA recognition and further clarifies the roles of, water molecules near residues 50 and 51.
About this Structure
2HDD is a Single protein structure of sequence from Drosophila melanogaster. Full crystallographic information is available from OCA.
Reference
Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity., Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE, Sauer RT, Pabo CO, Structure. 1997 Aug 15;5(8):1047-54. PMID:9309220
Page seeded by OCA on Wed Nov 21 11:41:16 2007
