PDBsum entry 3ikt

DNA binding protein/DNA

PDB id: 3ikt

Contents

Protein chains

204 a.a. *

DNA/RNA

Ligands

NAD

Waters ×378

* Residue conservation analysis

PDB id:

3ikt

Name:

DNA binding protein/DNA

Title:

Crystal structure of a rex-family repressor/DNA/NAD+ complex from thermus aquaticus

Structure:

Redox-sensing transcriptional repressor rex. Chain: a, b. Engineered: yes. Rex operator DNA. Chain: c, d. Engineered: yes. Other_details: the minimal consensus binding site of some rex family members

Source:

Thermus thermophilus hb27. Organism_taxid: 262724. Strain: hb27 / dsm 7039. Atcc: baa-163. Gene: rex, tt_c1293. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic 22bp dsdna obtained from idt

Resolution:

2.26Å R-factor: 0.234 R-free: 0.268

Authors:

K.J.Mclaughlin,C.L.Kielkopf

Key ref:

K.J.McLaughlin et al. (2010). Structural basis for NADH/NAD+ redox sensing by a Rex family repressor. Mol Cell, 38, 563-575. PubMed id: 20513431

Date:

06-Aug-09 Release date: 09-Jun-10

Protein chains

Q72I39  (REX_THET2) -  Redox-sensing transcriptional repressor Rex from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 211 a.a.

Struc: 204 a.a.

DNA/RNA chains

C-G-C-T-G-T-G-A-A-C-G-C-G-T-T-C-A-C-A-G-C-G 22 bases

C-G-C-T-G-T-G-A-A-C-G-C-G-T-T-C-A-C-A-G-C-G 22 bases

Mol Cell 38:563-575 (2010)

PubMed id: 20513431

Structural basis for NADH/NAD+ redox sensing by a Rex family repressor.

K.J.McLaughlin, C.M.Strain-Damerell, K.Xie, D.Brekasis, A.S.Soares, M.S.Paget, C.L.Kielkopf.

ABSTRACT

Nicotinamide adenine dinucleotides have emerged as key signals of the cellular redox state. Yet the structural basis for allosteric gene regulation by the ratio of reduced NADH to oxidized NAD(+) is poorly understood. A key sensor among Gram-positive bacteria, Rex represses alternative respiratory gene expression until a limited oxygen supply elevates the intracellular NADH:NAD(+) ratio. Here we investigate the molecular mechanism for NADH/NAD(+) sensing among Rex family members by determining structures of Thermus aquaticus Rex bound to (1) NAD(+), (2) DNA operator, and (3) without ligand. Comparison with the Rex/NADH complex reveals that NADH releases Rex from the DNA site following a 40 degrees closure between the dimeric subunits. Complementary site-directed mutagenesis experiments implicate highly conserved residues in NAD-responsive DNA-binding activity. These rare views of a redox sensor in action establish a means for slight differences in the nicotinamide charge, pucker, and orientation to signal the redox state of the cell.