PDBsum entry: 3dfv

Transcription/DNA

PDB id: 3dfv

Contents

Protein chains

56 a.a. *

DNA/RNA

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

3dfv

Name:

Transcription/DNA

Title:

Adjacent gata DNA binding

Structure:

Trans-acting t-cell-specific transcription factor gata-3. Chain: d, c. Fragment: unp residues 308-370. Synonym: gata-binding factor 3. Engineered: yes. DNA (5'- d( Dtp Dtp Dcp Dtp Dgp Dap Dtp Dap Dap Dgp Dap Dcp Dtp Dtp Dap Dtp Dcp Dtp Dgp Dc)-3').

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: gata3, gata-3. Expressed in: escherichia coli. Synthetic: yes. Synthetic: yes

Resolution:

3.10Å R-factor: 0.276 R-free: 0.289

Authors:

D.L.Bates,G.K.Kim,L.Guo,L.Chen

Key ref:

D.L.Bates et al. (2008). Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA. J Mol Biol, 381, 1292-1306. PubMed id: 18621058 DOI: 10.1016/j.jmb.2008.06.072

Date:

12-Jun-08 Release date: 29-Jul-08

Protein chains

P23772  (GATA3_MOUSE) -  Trans-acting T-cell-specific transcription factor GATA-3

Seq: 443 a.a.

Struc: 56 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: transcription factor activity (3 terms)

DOI no: 10.1016/j.jmb.2008.06.072

J Mol Biol 381:1292-1306 (2008)

PubMed id: 18621058

Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA.

D.L.Bates, Y.Chen, G.Kim, L.Guo, L.Chen.

ABSTRACT

The GATA family of transcription factors (GATA1-6) binds selected GATA sites in vertebrate genomes to regulate specific gene expression. Although vertebrate GATA factors have two highly conserved zinc finger motifs, how the two fingers act together to recognize functional DNA elements is not well understood. Here we determined the crystal structures of the C-terminal zinc finger of mouse GATA3 bound to DNA containing two variously arranged GATA binding sites. Our structures and accompanying biochemical analyses reveal two distinct modes of DNA binding by GATA to closely arranged sites. One mode involves cooperative binding by two GATA factors that interact with each other through protein-protein interactions. The other involves simultaneous binding of the N-terminal zinc finger (N-finger) and the C-terminal zinc finger of the same GATA factor. Our studies represent the first crystallographic analysis of GATA zinc fingers bound to DNA and provide new insights into the DNA recognition mechanism by the GATA zinc finger. Our crystal structure also reveals a dimerization interface in GATA that has previously been shown to be important for GATA self-association. These findings significantly advance our understanding of the structure and function of GATA and provide an important framework for further investigating the in vivo mechanisms of GATA-dependent gene regulation.

Selected figure(s)

Figure 3.
Fig. 3. Structural basis of GATA3 C-finger dimerization. (a) Surface model of the GATA3 C-finger dimer bound to the ADJ DNA showing the extended protein/DNA and protein–protein interaction interfaces. The transparent surfaces are colored according to the underling ribbon/stick/atom model. The orientation is similar to that of Fig. 1b. (b) Detailed view of the main dimerization interface formed by the NRPL motif. Here Pro353 and Thr355 engage in extensive van der Waals contacts, while Arg352 interacts with the DNA backbone to stabilize the conformation of the NRPL motif. Several contacts are indicated by dashed lines to give a distance scale. (c) Close contacts between the C-terminal basic tail of one zinc finger in alternative conformation (cyan) with the recognition helix of another zinc finger bound to the adjacent major groove.

Figure 5.
Fig. 5. Diverse modes of DNA binding to different double-GATA sites by GATA factors. A model of GATA3 DF is built wherein the N-finger (green) is constructed by homology modeling based on the crystal structure of the C-finger (purple). The linker region is assumed to be flexible and may adopt different conformations depending on the arrangement of the double-GATA sites. (a) Model of GATA3 DF bound to double-GATA site resembling the ADJ DNA. (b) Model of GATA3 DF bound to the GATA/GATC composite site (OPP A–C) DNA or palindromic double-GATA site at low protein concentrations. (c) Model of GATA3 DF bound to palindromic double-GATA site at high protein concentrations. The three models were constructed based on EMSA data of Fig. 4 and were meant to interpret the specific DNA binding interactions by the N-finger and the C-finger on different probes and under different conditions. The conformation of the linker region, and whether the N-finger interacts with the C-finger or DNA nonspecifically in (a) and (c), cannot be determined with current data and are therefore hypothetical in the figure.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 1292-1306) copyright 2008.

Figures were selected by the author.