PDBsum entry: 2dgc

Transcription/DNA

PDB id: 2dgc

Contents

Protein chain

49 a.a. *

DNA/RNA

Waters ×46

* Residue conservation analysis

PDB id:

2dgc

Name:

Transcription/DNA

Title:

Gcn4 basic domain, leucine zipper complexed with atf/creb site DNA

Structure:

DNA (5'- d( Tp Gp Gp Ap Gp Ap Tp Gp Ap Cp Gp Tp Cp Ap Tp Cp T p Cp C)-3'). Chain: b. Engineered: yes. Protein (gcn4). Chain: a

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.214 R-free: 0.316

Authors:

W.Keller,P.Koenig,T.J.Richmond

Key ref:

W.Keller et al. (1995). Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition. J Mol Biol, 254, 657-667. PubMed id: 7500340 DOI: 10.1006/jmbi.1995.0645

Date:

28-Sep-95 Release date: 08-Mar-96

Protein chain

P03069  (GCN4_YEAST) -  General control protein GCN4

Seq: 281 a.a.

Struc: 49 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: nucleic acid binding (4 terms)

DOI no: 10.1006/jmbi.1995.0645

J Mol Biol 254:657-667 (1995)

PubMed id: 7500340

Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.

W.Keller, P.König, T.J.Richmond.

ABSTRACT

The X-ray structure of the GCN4-bZIP protein bound to DNA containing the ATF/CREB recognition sequence has been refined at 2.2 A. The water-mediated interactions between the basic domain and DNA are revealed, and combined with a more accurate description of the direct contacts, further clarify how binding specificity is achieved. Water molecules extend the interactions of both invariant basic domain residues, asparagine 235 and arginine 243, beyond their direct base contacts. The slight bending of the basic domain alpha-helix around the DNA facilitates the linking of arginine 241, 243 and 245 to main-chain carbonyl oxygen atoms via water molecules, apparently stabilizing interactions with the DNA.

Selected figure(s)

Figure 1.
Figure 1. The protein and DNA sequences of the complex crystallized and interaction summary. A, GCN4-bZIP domain numbered according to the full-length sequence. Residues that make one or more DNA contacts are indicated: b, direct to base; w, via water to base; p, direct to phosphate; x, via water to phosphate. B, Self-complementary, 18 bp palindromic ATF/CREB DNA with terminal thymidine. A molecular and crystallographic 2-fold axis passes through the C-1 G1 base step. The specific recognition sequence is marked with the bar. C, Protein-DNA interaction summary for one basic domain and DNA half-site. The location of the 2-fold axis is indicated. Direct and water (W) mediated interactions with bases are shown as continuous lines, interactions with the phosphate backbone as broken lines and hydrophobic interactions as dotted lines. Arrows indicate the direction of hydrogen bonds.

Figure 4.
Figure 4. Stereo diagrams of the base-specific interactions. The views are down the overall DNA helix axis, and hydrogen bonds (broken) and hydrophobic contacts (dotted) are indicated. A, Interaction of Asp235 with three consecutive base-pairs and the hydrophobic contacts of the T-4 methyl group. B, Interactions at the central CG base-pairs. Arg243 forms an arginine helix bridge with the carbonyl group of Thr235 while making multiple interactions with the DNA (27). Arg240 bridges between the C-1 and G1 phosphate groups of the same DNA strand. The C-1 deoxyribose moeity has the C3' endo conformation with a pucker angle of 53.4°. C, Water-mediated interaction of Lys246 with base G-3 and the hydrophobic contacts of the T2 methyl group.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 254, 657-667) copyright 1995.

Figures were selected by an automated process.