PDBsum entry 2er8

Transcription activator/DNA

PDB id: 2er8

Contents

Protein chains

68 a.a. *

64 a.a. *

DNA/RNA

Metals

_ZN ×8

Waters ×33

* Residue conservation analysis

PDB id:

2er8

Name:

Transcription activator/DNA

Title:

Crystal structure of leu3 DNA-binding domain complexed with a 12mer DNA duplex

Structure:

5'-d( Cp Cp Cp Gp Gp Tp Ap Cp Cp Gp Gp G)-3'. Chain: e, f, g, h. Engineered: yes. Regulatory protein leu3. Chain: a, b, c, d. Fragment: residues 32-103. Engineered: yes

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: leu3 (32-103). Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.85Å R-factor: 0.237 R-free: 0.265

Authors:

M.X.Fitzgerald,R.Marmorstein

Key ref:

M.X.Fitzgerald et al. (2006). Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein. Structure, 14, 725-735. PubMed id: 16615914 DOI: 10.1016/j.str.2005.11.025

Date:

24-Oct-05 Release date: 04-Apr-06

Protein chains

P08638  (LEUR_YEAST) -  Regulatory protein LEU3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 886 a.a.

Struc: 68 a.a.

Protein chain

P08638  (LEUR_YEAST) -  Regulatory protein LEU3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 886 a.a.

Struc: 64 a.a.

DNA/RNA chains

C-C-C-G-G-T-A-C-C-G-G-G 12 bases

C-C-C-G-G-T-A-C-C-G-G-G 12 bases

C-C-C-G-G-T-A-C-C-G-G-G 12 bases

C-C-C-G-G-T-A-C-C-G-G-G 12 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.?

DOI no: 10.1016/j.str.2005.11.025

Structure 14:725-735 (2006)

PubMed id: 16615914

Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein.

M.X.Fitzgerald, J.R.Rojas, J.M.Kim, G.B.Kohlhaw, R.Marmorstein.

ABSTRACT

Gal4 is the prototypical Zn2Cys6 binuclear cluster transcriptional regulator that binds as a homodimer to DNA containing inverted CGG half-sites. Leu3, a member of this protein family, binds to everted (opposite polarity to inverted) CGG half-sites, and an H50C mutation within the Leu3 Zn2Cys6 binuclear motif abolishes its transcriptional repression function without impairing DNA binding. We report the X-ray crystal structures of DNA complexes with Leu3 and Leu3(H50C) and solution DNA binding studies of selected Leu3 mutant proteins. These studies reveal the molecular details of everted CGG half-site recognition, and suggest a role for the H50C mutation in transcriptional repression. Comparison with the Gal4-DNA complex shows an unexpected conservation in the DNA recognition mode of inverted and everted CGG half-sites, and points to a critical function of a linker region between the Zn2Cys6 binuclear cluster and dimerization regions in DNA binding specificity. Broader implications of these findings are discussed.

Selected figure(s)

Figure 2.
Figure 2. Overall Structure of Leu3-DNA Complexes
(A) DNA sequences used for crystallization. Half-sites recognized in the structure are in bold. Half of each 12-mer duplex that the complex straddles is shown, and designed half-sites are underlined.
(B) Structures of Leu3-DNA complexes. The DNA (red or orange), half-sites (gray), zincs (yellow), and subunits of the homodimer (cyan or blue) are color-coded.
(C) Cα overlay of Leu3 structures. The Leu3/15-mer is in blue, the Leu3(H50C)/15-mer is in green, and the Leu3/12-mer is in red.
(D) Electron density map around the H50C loop of the Leu3(H50C)-DNA complex is shown with a contour of one sigma in gray. Each complex is color-coded: Leu3/15-mer (green), Leu3(H50C)/15-mer (blue), and Leu3/12-mer (orange). Figure 2. Overall Structure of Leu3-DNA Complexes(A) DNA sequences used for crystallization. Half-sites recognized in the structure are in bold. Half of each 12-mer duplex that the complex straddles is shown, and designed half-sites are underlined.(B) Structures of Leu3-DNA complexes. The DNA (red or orange), half-sites (gray), zincs (yellow), and subunits of the homodimer (cyan or blue) are color-coded.(C) Cα overlay of Leu3 structures. The Leu3/15-mer is in blue, the Leu3(H50C)/15-mer is in green, and the Leu3/12-mer is in red.(D) Electron density map around the H50C loop of the Leu3(H50C)-DNA complex is shown with a contour of one sigma in gray. Each complex is color-coded: Leu3/15-mer (green), Leu3(H50C)/15-mer (blue), and Leu3/12-mer (orange).

Figure 3.
Figure 3. Protein-DNA Contacts within the Leu3-DNA Complex
(A) Schematic diagram of protein-DNA contacts in the Leu3/15-mer complex. Blue and cyan color-code the two subunits of the dimer. DNA half-sites are colored in gray, while other DNA bases are colored in red. Protein arrows distinguish between base and phosphate interactions and, if a backbone atom is not specified, a side chain is making the interaction. Water-mediated contacts have been omitted for clarity.
(B) Overall Leu3/15-mer complex with dark black boxes and letters in italics to indicate the regions that will be enlarged in the subsequent panels.
(C) Close-up of the interaction between residues K78 and R79 of the Leu3 coiled-coil and the DNA. Subunits of the homodimer are colored in blue and cyan. The DNA (red), half-sites (gray), residues (yellow), and hydrogen bonds (green) are also color-coded.
(D) Close-up of the interaction between residues V38, Q42, and F73 of the Leu3 protein. Surface area from the van der Waals surface of the residues is translucent and light blue.
(E) Close-up of the interaction between residues K44/Y77 and DNA. Figure 3. Protein-DNA Contacts within the Leu3-DNA Complex(A) Schematic diagram of protein-DNA contacts in the Leu3/15-mer complex. Blue and cyan color-code the two subunits of the dimer. DNA half-sites are colored in gray, while other DNA bases are colored in red. Protein arrows distinguish between base and phosphate interactions and, if a backbone atom is not specified, a side chain is making the interaction. Water-mediated contacts have been omitted for clarity.(B) Overall Leu3/15-mer complex with dark black boxes and letters in italics to indicate the regions that will be enlarged in the subsequent panels.(C) Close-up of the interaction between residues K78 and R79 of the Leu3 coiled-coil and the DNA. Subunits of the homodimer are colored in blue and cyan. The DNA (red), half-sites (gray), residues (yellow), and hydrogen bonds (green) are also color-coded.(D) Close-up of the interaction between residues V38, Q42, and F73 of the Leu3 protein. Surface area from the van der Waals surface of the residues is translucent and light blue.(E) Close-up of the interaction between residues K44/Y77 and DNA.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 725-735) copyright 2006.

Figures were selected by an automated process.