PDBsum entry: 5gat

Transcription/DNA

PDB id: 5gat

Contents

Protein chain

66 a.a. *

DNA/RNA

Metals

_ZN

* Residue conservation analysis

PDB id:

5gat

Name:

Transcription/DNA

Title:

Solution nmr structure of the wild type DNA binding domain of area complexed to a 13bp DNA containing a cgata site, 35 structures

Structure:

DNA (5'- d( Cp Ap Gp Cp Gp Ap Tp Ap Gp Ap Gp Ap C)-3'). Chain: b. Engineered: yes. DNA (5'- d( Gp Tp Cp Tp Cp Tp Ap Tp Cp Gp Cp Tp G)-3'). Chain: c. Engineered: yes. Nitrogen regulatory protein area.

Source:

Synthetic: yes. Emericella nidulans. Organism_taxid: 162425. Organ: tail. Gene: potential. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

35 models

Authors:

G.M.Clore,M.Starich,M.Wikstrom,A.M.Gronenborn

Key ref:

M.R.Starich et al. (1998). The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors. J Mol Biol, 277, 605-620. PubMed id: 9533883 DOI: 10.1006/jmbi.1998.1625

Date:

07-Nov-97 Release date: 28-Jan-98

Protein chain

P17429  (AREA_EMENI) -  Nitrogen regulatory protein areA

Seq: 876 a.a.

Struc: 66 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

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

DOI no: 10.1006/jmbi.1998.1625

J Mol Biol 277:605-620 (1998)

PubMed id: 9533883

The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors.

M.R.Starich, M.Wikström, H.N.Arst, G.M.Clore, A.M.Gronenborn.

ABSTRACT

The solution structure of a complex between the DNA binding domain of a fungal GATA factor and a 13 base-pair oligonucleotide containing its physiologically relevant CGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy. The AREA DNA binding domain, from Aspergillus nidulans, possesses a single Cys2-Cys2 zinc finger module and a basic C-terminal tail, which recognize the CGATAG element via an extensive network of hydrophobic interactions with the bases in the major groove and numerous non-specific contacts along the sugar-phosphate backbone. The zinc finger core of the AREA DNA binding domain has the same global fold as that of the C-terminal DNA binding domain of chicken GATA-1. In contrast to the complex with the DNA binding domain of GATA-1 in which the basic C-terminal tail wraps around the DNA and lies in the minor groove, the structure of complex with the AREA DNA binding domain reveals that the C-terminal tail of the fungal domain runs parallel with the sugar phosphate backbone along the edge of the minor groove. This difference is principally attributed to amino acid substitutions at two positions of the AREA DNA binding domain (Val55, Asn62) relative to that of GATA-1 (Gly55, Lys62). The impact of the different C-terminal tail binding modes on the affinity and specificity of GATA factors is discussed.

Selected figure(s)

Figure 4.
Figure 4. Four views illustrating the interaction of the AREA DBD with its cognate CGATAG target. The protein backbone is depicted as a red worm, while hydrophobic and hydrophilic side-chains participating in DNA recognition are shown in green and blue, respectively. Cysteine side-chains coordinating the zinc atom (pink sphere) are shown in yellow. For A and B the DNA is depicted as a molecular surface with the major groove colored light blue and the minor groove colored light red. In C a bond representation of the DNA is shown with A·T base-pairs in purple and G·C base-pairs in light blue. A bond representation for the DNA is also shown in D with all base-pairs in light blue.

Figure 5.
Figure 5. Stereoviews showing specific and non-specific interactions between AREA DBD side-chains and the DNA. The protein backbone is shown in red, hydrophobic side-chains in green and hydrophilic side-chains in dark blue. In each case, A·T base-pairs are colored purple and G·C base-pairs are colored light blue.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 277, 605-620) copyright 1998.

Figures were selected by the author.