Conserved structural features of ETS domain-DNA complexes
- 49 Downloads
ETS proteins are a family of widespread transcription factors that regulate the expression of many animal genes. Structurally, ETS proteins are characterized by a conserved DNA-binding ETS domain, which recognizes DNA sequences containing the trinucleotide GGA. The structural features of ETS domain-DNA complexes were analyzed, and conserved contacts important in terms of interaction stability and specificity were identified. The analysis revealed nine conserved hydrogen bonds with oxygens of DNA backbone phosphates, two bidentate hydrogen bonds with DNA major groove atoms, one conserved hydrophobic cluster located on the protein-DNA interface and important for binding site recognition, and 12 conserved water molecules presumably mediating the ETS domain-DNA interaction. The results are represented in specialized data bank of protein-DNA complexes (NPIDB).
Key wordsETS family protein-DNA interaction comparative analysis of related structures eukaryotic transcription factor
Unable to display preview. Download preview PDF.
- 12.Krissinel E., Henrick K. 2004. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst. 60, 2256–2268.Google Scholar
- 13.Nicholas K.B., Nicholas H.B. Jr., Deerfield D.W. 1997. GeneDoc: Analysis and visualization of genetic variation. EMBNEW News. 4, 1–4.Google Scholar
- 15.DeLano W.L. 2003. The PyMOL Molecular Graphics System. San Carlos, CA: DeLano Scientific.Google Scholar
- 16.Alexeevski A., Spirin S., Alexeevski D., Klychnikov O., Ershova A., Titov M., Karyagina A. 2004. CluD, a program for the determination of hydrophobic clusters in 3D structures of protein and protein-nucleic acids complexes. Biofizika (Moscow). 48,Suppl. 1, 146–156.Google Scholar
- 24.Karyagina A., Ershova A., Spirin S., Alexeevski A. 2005. The role of water in homeodomain-DNA interaction. In: Bioinformatics of Genome Regulation and Structure. Eds Kolchanov N., Hofestaedt R. N.Y.: Springer Science + Business Media, Inc., pp. 247–257.Google Scholar