THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves

THAP-family C(2)CH zinc-coordinating DNA-binding proteins function in diverse eukaryotic cellular processes, such as transposition, transcriptional repression, stem-cell pluripotency, angiogenesis and neurological function. To determine the molecular basis for sequence-specific DNA recognition by TH...

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Published inNature structural & molecular biology Vol. 17; no. 1; pp. 117 - 123
Main Authors Corn, Jacob E, Rio, Donald C, Sabogal, Alex, Berger, James M, Lyubimov, Artem Y
Format Journal Article
LanguageEnglish
Published United States Nature Publishing Group 01.01.2010
Subjects
Amino Acid Sequence
Animals
Base Sequence
Binding sites
Cellular proteins
Chromatography, Gel
Crystallization
Deoxyribonucleic acid
DNA
DNA - metabolism
DNA Primers - genetics
DNA-Binding Proteins - chemistry
DNA-Binding Proteins - genetics
DNA-Binding Proteins - metabolism
Drosophila melanogaster
Drosophila melanogaster - enzymology
Electrophoretic Mobility Shift Assay
Gene targeting
Genetic aspects
Models, Molecular
Molecular Sequence Data
Mutagenesis
Properties
Protein Binding
Protein Conformation
Protein Structure, Tertiary - genetics
Proteins
Sequence Analysis, DNA
Transposases - chemistry
Transposases - genetics
Transposases - metabolism
United States
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Summary:THAP-family C(2)CH zinc-coordinating DNA-binding proteins function in diverse eukaryotic cellular processes, such as transposition, transcriptional repression, stem-cell pluripotency, angiogenesis and neurological function. To determine the molecular basis for sequence-specific DNA recognition by THAP proteins, we solved the crystal structure of the Drosophila melanogaster P element transposase THAP domain (DmTHAP) in complex with a natural 10-base-pair site. In contrast to C(2)H(2) zinc fingers, DmTHAP docks a conserved beta-sheet into the major groove and a basic C-terminal loop into the adjacent minor groove. We confirmed specific protein-DNA interactions by mutagenesis and DNA-binding assays. Sequence analysis of natural and in vitro-selected binding sites suggests that several THAPs (DmTHAP and human THAP1 and THAP9) recognize a bipartite TXXGGGX(A/T) consensus motif; homology suggests THAP proteins bind DNA through a bipartite interaction. These findings reveal the conserved mechanisms by which THAP-family proteins engage specific chromosomal target elements.
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These authors contributed equally to this work.
ISSN:1545-9993
1545-9985
DOI:10.1038/nsmb.1742