PDBsum entry 3kde

DNA binding protein/DNA

PDB id: 3kde

Contents

Protein chain

75 a.a. *

DNA/RNA

Metals

_ZN

Waters ×107

* Residue conservation analysis

PDB id:

3kde

Name:

DNA binding protein/DNA

Title:

Crystal structure of the thap domain from d. Melanogaster p-element transposase in complex with its natural DNA binding site

Structure:

5'-d( Gp Tp Tp Ap Ap Gp (Bru)p Gp Gp A)-3'. Chain: a. Engineered: yes. Other_details: 5'-gttaag(brdu)gga-3'. 5'-d( (Bru)p Cp Cp Ap Cp Tp Tp Ap Ap C)-3'. Chain: b. Engineered: yes. Other_details: 5'-(brdu)ccacttaac-3'. Transposable element p transposase.

Source:

Synthetic: yes. Other_details: synthetic brominated ssdna oligo. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: t. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.74Å R-factor: 0.179 R-free: 0.216

Authors:

A.Sabogal,A.Y.Lyubimov,J.M.Berger,D.C.Rio

Key ref:

A.Sabogal et al. (2010). THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Nat Struct Biol, 17, 117-123. PubMed id: 20010837

Date:

22-Oct-09 Release date: 08-Dec-09

Protein chain

Q7M3K2  (PELET_DROME) -  Transposable element P transposase from Drosophila melanogaster

Seq: 751 a.a.

Struc: 75 a.a.

DNA/RNA chains

G-T-T-A-A-G-BRU-G-G-A 10 bases

BRU-C-C-A-C-T-T-A-A-C 10 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.- - ?????

Nat Struct Biol 17:117-123 (2010)

PubMed id: 20010837

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

A.Sabogal, A.Y.Lyubimov, J.E.Corn, J.M.Berger, D.C.Rio.

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.