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

PDB-id

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

Class

transcription-DNA

Method

NMR

Summary

Determination of the three-dimensional structure of the mrf2-DNA complex using paramagnetic spin labeling

Reference

Cai S, Zhu L, Zhang Z, Chen Y (2007): "Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling." Biochemistry, 46, 4943-4950. doi: 10.1021/bi061738h.

Abstract

Understanding the mechanism of protein-DNA interactions at the molecular level is one of the main focuses in structural and molecular biological investigations. At present, NMR spectroscopy is the only approach that can provide atomic details of protein-DNA recognition in solution. However, determining the structures of protein-DNA complexes using NMR spectroscopy has been dependent on the observation of intermolecular nuclear Overhauser effects (NOE) and their assignments, which are difficult to obtain in many cases. In this study, we have shown that intermolecular distance constraints derived from a single spin-label in combination with docking calculations have defined many specific contacts of the complex between the AT-rich interaction domain (ARID) of Mrf2 and its target DNA. Mrf2 contacts DNA mainly using the two flexible loops, L1 and L2. While the L1 loop contacts the phosphate backbone, L2 and several residues in the adjacent helices interact with AT base pairs in the major groove of DNA. Despite the structural diversity in the ARID family of DNA-binding proteins, Mrf2 maintains contacts with DNA similar to those observed in the homologous Dri-DNA complex.