3KDE

Crystal structure of the THAP domain from D. melanogaster P-element transposase in complex with its natural DNA binding site

Summary for 3KDE

• Entry DOI: 10.2210/pdb3kde/pdb
• Descriptor: 5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3', 5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3', Transposable element P transposase, ... (5 entities in total)
• Functional Keywords: thap domain, dna-binding domain, zinc-finger, beta-alpha-beta, p-element transposase, dna integration, dna recombination, dna-binding, metal-binding, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Drosophila melanogaster (Fruit fly); More
• Total number of polymer chains: 3
• Total formula weight: 14969.44

Authors

Sabogal, A.,Lyubimov, A.Y.,Berger, J.M.,Rio, D.C. (deposition date: 2009-10-22, release date: 2009-12-08, Last modification date: 2024-02-21)

Primary citation

Sabogal, A.,Lyubimov, A.Y.,Corn, J.E.,Berger, J.M.,Rio, D.C.
THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.
Nat.Struct.Mol.Biol., 17:117-123, 2010

PubMed Abstract: 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.

PubMed: 20010837
DOI: 10.1038/nsmb.1742

Experimental method

X-RAY DIFFRACTION (1.74 Å)