A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers

J Biol Chem. 2013 Dec 6;288(49):35180-91. doi: 10.1074/jbc.M113.482075. Epub 2013 Oct 6.


Myelin transcription factor 1 (MyT1/NZF2), a member of the neural zinc-finger (NZF) protein family, is a transcription factor that plays a central role in the developing central nervous system. It has also recently been shown that, in combination with two other transcription factors, the highly similar paralog MyT1L is able to direct the differentiation of murine and human stem cells into functional neurons. MyT1 contains seven zinc fingers (ZFs) that are highly conserved throughout the protein and throughout the NZF family. We recently presented a model for the interaction of the fifth ZF of MyT1 with a DNA sequence derived from the promoter of the retinoic acid receptor (RARE) gene. Here, we have used NMR spectroscopy, in combination with surface plasmon resonance and data-driven molecular docking, to delineate the mechanism of DNA binding for double ZF polypeptides derived from MyT1. Our data indicate that a two-ZF unit interacts with the major groove of the entire RARE motif and that both fingers bind in an identical manner and with overall two-fold rotational symmetry, consistent with the palindromic nature of the target DNA. Several key residues located in one of the irregular loops of the ZFs are utilized to achieve specific binding. Analysis of the human and mouse genomes based on our structural data reveals three putative MyT1 target genes involved in neuronal development.

Keywords: Computer Modeling; Myelin; Nuclear Magnetic Resonance; Protein Structure; Zinc Finger.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Binding Sites / genetics
  • DNA / genetics
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Humans
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Neurogenesis
  • Neurons / cytology
  • Neurons / metabolism
  • Nuclear Magnetic Resonance, Biomolecular
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Conformation
  • Receptors, Retinoic Acid / genetics
  • Sequence Homology, Amino Acid
  • Sequence Homology, Nucleic Acid
  • Surface Plasmon Resonance
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Zinc Fingers


  • DNA-Binding Proteins
  • MYT1 protein, human
  • Myt1 protein, mouse
  • Receptors, Retinoic Acid
  • Transcription Factors
  • DNA

Associated data

  • PDB/2MF8