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Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.
Yonghong Zhang1, Christine A Larsen, H Scott Stadler
1Department of Chemistry, University of California Davis, Davis, California, United States of America.
Plos One
|August 11, 2011
Summary
The HOXA13 homeodomain dimer binds DNA via its N-terminal arm and C-terminal helix, with V373 crucial for TAA sequence recognition. Dimerization is essential for HOXA13
Area of Science:
- Molecular Biology
- Structural Biology
- Genetics
Background:
- Homeobox genes, like HOXA13, encode transcription factors regulating embryonic development.
- HOXA13 controls gene expression by binding to AT-rich DNA sequences.
Purpose of the Study:
- To determine the NMR structure of the HOXA13 homeodomain (A13DBD) bound to DNA.
- To elucidate the molecular mechanisms of HOXA13 DNA binding and transcriptional activation.
Main Methods:
- Nuclear Magnetic Resonance (NMR) spectroscopy to determine protein-DNA complex structure.
- DNA binding assays to measure dissociation constants.
- Site-directed mutagenesis to assess the role of specific residues and dimerization.
Main Results:
- The HOXA13 homeodomain forms a dimer that binds an 11-mer DNA duplex with high affinity (Kd = 7.5 nM).
- The N-terminal arm interacts with the DNA minor groove, while the C-terminal helix recognizes the ATAA sequence in the major groove.
- Specific residues, including V373, are critical for DNA sequence recognition, and mutations impair DNA binding and transcriptional activity.
- The F344A mutation significantly weakens dimerization and reduces transcriptional activity by 76%.
Conclusions:
- HOXA13 dimerization is essential for its transcriptional activity.
- The non-conserved residue V373 plays a critical role in recognizing the TAA motif within the DNA major groove.
- Structural insights reveal how HOXA13 functions as a dimeric transcription factor in embryonic development.
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