PDBsum entry 3ezh

Transferase

PDB id: 3ezh

Contents

Protein chains

114 a.a. *

Ligands

NO3

Waters ×255

* Residue conservation analysis

PDB id:

3ezh

Name:

Transferase

Title:

Crystal structure of the e. Coli histidine kinase narx sensor domain in complex with nitrate

Structure:

Nitrate/nitrite sensor protein narx. Chain: a, b. Fragment: unp residues 38-151. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: b1222, jw1213, narr, narx. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.217 R-free: 0.258

Authors:

J.Cheung,W.A.Hendrickson

Key ref:

J.Cheung and W.A.Hendrickson (2009). Structural analysis of ligand stimulation of the histidine kinase NarX. Structure, 17, 190-201. PubMed id: 19217390 DOI: 10.1016/j.str.2008.12.013

Date:

22-Oct-08 Release date: 23-Dec-08

Protein chains

P0AFA2  (NARX_ECOLI) -  Nitrate/nitrite sensor protein NarX from Escherichia coli (strain K12)

Seq: 598 a.a.

Struc: 114 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.13.3 - histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2008.12.013

Structure 17:190-201 (2009)

PubMed id: 19217390

Structural analysis of ligand stimulation of the histidine kinase NarX.

J.Cheung, W.A.Hendrickson.

ABSTRACT

Histidine kinase receptors are a large family of membrane-spanning proteins found in many prokaryotes and some eukaryotes. They are a part of two-component signal transduction systems, which each comprise a sensor kinase and a response regulator and are involved with the regulation of many cellular processes. NarX is a histidine kinase receptor that responds to nitrate and nitrite to effect regulation of anaerobic respiration in various bacteria. We present high-resolution X-ray crystal structures of the periplasmic sensor domain from Escherichia coli NarX in a complex with nitrate and in the apo state. Our analysis reveals that nitrate-binding induces conformation changes that result in a piston-type displacement between the N- and C-terminal helices of the periplasmic domain. Such conformational changes might represent a conserved mechanism of signaling in histidine kinases by which ligand binding is communicated across the lipid bilayer.

Selected figure(s)

Figure 4.
Figure 4. Comparison of NarX[S] and Tar Dimers
(A) Worm representation of the dimeric aspartate receptor Tar, drawn in stereo. Subunits A and B of Tar (Yeh et al., 1996) are colored yellow and blue, respectively.
(B) Worm representation of NarX[s1] dimers in stereo. A “Tar-like” NarX[s] dimer is formed when subunits A (yellow) and B (blue) from NarX[s1](NO[3]) are independently superimposed upon subunits A and B of Tar, respectively. Subunit B from the natural NarX[s] dimer of Figure 1 is shown in gray. The black vertical line represents the quasi two-fold rotation axis of the observed dimer. The red line shows the resulting axis of 9.3° rotation that relates B subunits from the natural, observed NarX[S]dimer and the constructed Tar-like NarX[s] dimer. In the orientation of the molecules shown, the red rotation axis intersects the black rotation axis and is angled approximately 30 degrees above the plane of the figure.

Figure 5.
Figure 5. Structure of NarX[S](apo)
The overall structure of NarX[S2] in a nitrate-free state is shown as a ribbon diagram. Each monomer is colored individually and labeled with the PDB chain identifier (PDB code 3EZI).

The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 190-201) copyright 2009.

Figures were selected by an automated process.