Solution structure of a mutant of transcription factor 1: Implications forenhanced DNA binding

An NMR solution structure of a mutant of the homodimer protein transcriptio n factor 1, TF1-G15/I32 (22 kDa), has been solved to atomic resolution, wit h 23 final structures that converge to an r.m.s.d. of 0.78 Angstrom. The ov erall shape of TF1-G15/I32 remains similar to that of the wild-type protein and other type LI DNA-binding proteins. Each monomer has two N-terminal al pha-helices separated by a short loop, followed by a three-stranded beta-sh eet, whose extension between the second and third beta-strands forms an ant iparallel beta-ribbon arm, leading to a C-terminal third alpha-helix that i s severely kinked in the middle. Close examination of the structure of TF1- G15/I32 reveals why it is more stable and binds DNA more tightly than does its wild-type counterpart. The dimeric core, consisting of the N-terminal h elices and the beta-sheets, is more tightly packed, and this might be respo nsible for its increased thermal stability. The DNA-binding domain, compose d of the top face of the beta-sheet, the beta-ribbon arms and the C-termina l helices, is little changed from wildtype TF1. Rather, the enhancement in DNA affinity must be due almost exclusively to the creation of an additiona l DNA-binding site at the side of the dimer by changes affecting helices 1 and 2: helix 2 of TF1-G15/I32 is one residue longer than helix 2 of the wil d-type protein, bends inward, and is both translationally and rotationally displaced relative to helix 1. This rearrangement creates a longer, narrowe r fissure between the V-shaped N-terminal helices and exposes additional po sitively charged surface at each side of the dimer. (C) 2000 Academic Press .