PDBsum entry 2eux

Cell cycle/DNA

PDB id: 2eux

Contents

Protein chain

290 a.a. *

DNA/RNA

Waters ×349

* Residue conservation analysis

PDB id:

2eux

Name:

Cell cycle/DNA

Title:

Structure of a ndt80-DNA complex (mse variant va4g)

Structure:

5'-d( Tp Gp Cp Gp Ap Cp Gp Cp Ap Ap Ap Ap Ap C)-3'. Chain: b. Engineered: yes. Other_details: mutant mse DNA strand 1. 5'-d( Ap Gp Tp Tp Tp Tp Tp Gp Cp Gp Tp Cp Gp C)-3'. Chain: c. Engineered: yes. Other_details: mutant mse DNA strand 2. Ndt80 protein.

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ndt80. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Trimer (from PQS)

Resolution:

1.57Å R-factor: 0.173 R-free: 0.203

Authors:

J.S.Lamoureux,J.N.Glover

Key ref:

J.S.Lamoureux and J.N.Glover (2006). Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes. Structure, 14, 555-565. PubMed id: 16531239 DOI: 10.1016/j.str.2005.11.017

Date:

30-Oct-05 Release date: 21-Mar-06

Protein chain

P38830  (NDT80_YEAST) -  Meiosis-specific transcription factor NDT80 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 627 a.a.

Struc: 290 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

T-G-C-G-A-C-G-C-A-A-A-A-A-C 14 bases

A-G-T-T-T-T-T-G-C-G-T-C-G-C 14 bases

DOI no: 10.1016/j.str.2005.11.017

Structure 14:555-565 (2006)

PubMed id: 16531239

Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes.

J.S.Lamoureux, J.N.Glover.

ABSTRACT

The Saccharomyces cerevisiae transcription factor Ndt80 selectively binds a DNA consensus sequence (the middle sporulation element [MSE]) to activate gene expression after the successful completion of meiotic recombination. Here we report the X-ray crystal structures of Ndt80 bound to ten distinct MSE variants. Comparison of these structures with the structure of Ndt80 bound to a consensus MSE reveals structural principles that determine the DNA binding specificity of this transcription factor. The 5' GC-rich end of the MSE contains distinct 5'-YpG-3' steps that are recognized by arginine side chains through a combination of hydrogen bonding and cation-pi interactions. The 3' AT-rich region is recognized via minor groove contacts that sterically exclude the N2 atom of GC base pairs. The conformation of the AT-rich region is fixed by interactions with the protein that favor recognition of poly(A)-poly(T) versus mixed AT sequences through an avoidance of major groove steric clashes at 5'-ApT-3' steps.

Selected figure(s)

Figure 4.
Figure 4. Stereoview of the Changes in the mC5T Structure
The mutation of the guanine recognized by Arg177 to an adenosine forces the side chain to reorient, displacing two water molecules. The wild-type structure is semitransparent, and illustrated in orange and teal for DNA and protein, respectively; waters are red and hydrogen bonds are yellow. The mutant structure is colored blue and purple for DNA and protein, respectively. The waters in the mutant are colored green and the hydrogen bonds are beige. The surface of the protein, excluding the side chain for Arg177, from the mutant structure is rendered in grey and is essentially identical to that of the wild-type structure.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 555-565) copyright 2006.

Figure was selected by the author.