PDBsum entry 1mn4

Transcription

PDB id: 1mn4

Contents

Protein chain

246 a.a. *

Waters ×89

* Residue conservation analysis

PDB id:

1mn4

Name:

Transcription

Title:

Structure of ndt80 (residues 59-340) DNA-binding domain core

Structure:

Ndt80 protein. Chain: a. Fragment: DNA-binding core (residues 59-340). Engineered: yes

Source:

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

Resolution:

2.20Å R-factor: 0.226 R-free: 0.268

Authors:

J.S.Lamoureux,D.Stuart,R.Tsang,C.Wu,J.N.M.Glover

Key ref:

J.S.Lamoureux et al. (2002). Structure of the sporulation-specific transcription factor Ndt80 bound to DNA. EMBO J, 21, 5721-5732. PubMed id: 12411490 DOI: 10.1093/emboj/cdf572

Date:

04-Sep-02 Release date: 06-Nov-02

Protein chain

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

Seq: 627 a.a.

Struc: 246 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/cdf572

EMBO J 21:5721-5732 (2002)

PubMed id: 12411490

Structure of the sporulation-specific transcription factor Ndt80 bound to DNA.

J.S.Lamoureux, D.Stuart, R.Tsang, C.Wu, J.N.Glover.

ABSTRACT

Progression through the middle phase of sporulation in Saccharomyces cerevisiae is promoted by the successful completion of recombination at the end of prophase I. Completion of meiotic recombination allows the activation of the sporulation-specific transcription factor Ndt80, which binds to a specific DNA sequence, the middle sporulation element (MSE), and activates approximately 150 genes to enable progression through meiosis. Here, we isolate the DNA-binding domain of Ndt80 and determine its crystal structure both free and in complex with an MSE-containing DNA. The structure reveals that Ndt80 is a member of the Ig-fold family of transcription factors. The structure of the DNA-bound form, refined at 1.4 A, reveals an unexpected mode of recognition of 5'-pyrimidine- guanine-3' dinucleotide steps by arginine residues that simultaneously recognize the 3'-guanine base through hydrogen bond interactions and the 5'-pyrimidine through stacking/van der Waals interactions. Analysis of the DNA-binding affinities of MSE mutants demonstrates the central importance of these interactions, and of the AT-rich portion of the MSE. Functional similarities between Ndt80 and the Caenorhabditis elegans p53 homolog suggest an evolutionary link between Ndt80 and the p53 family.

Selected figure(s)

Figure 6.
Figure 6 Schematic of Ndt80–DNA interactions. The MSE bases are highlighted in blue and are numbered 1–9. The complementary strand is distinguished with a prime following the number. Protein residues are colored as described in Figure 4. Electrostatic and polar interactions are indicated with arrows, while van der Waals contacts are represented by hash marks. The blue circles are water molecules that are highly ordered in the DNA–protein interface.

Figure 7.
Figure 7 5'-YpG-3' recognition by Ndt80. (A) View down the DNA helix axis showing base stacking between the C–G base pair at position 5 and the A–T pair at position 6. van der Waals surface representations of R177 (yellow), P57 (red) and T6' (gray) are displayed and hydrogen bonding interactions are indicated in green. (B) An equivalent CG–AT is shown from the structure of a similar DNA sequence determined in the absence of bound protein (Nelson et al., 1987). The view is such that the C–G base pairs in both panels are in identical orientations.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 5721-5732) copyright 2002.

Figures were selected by an automated process.