4IUK

Crystal structure of NreA of Staphylococcus carnosus with bound nitrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The NreA Protein Functions as a Nitrate Receptor in the Staphylococcal Nitrate Regulation System.

Niemann, V.Koch-Singenstreu, M.Neu, A.Nilkens, S.Gotz, F.Unden, G.Stehle, T.

(2014) J.Mol.Biol. 426: 1539-1553

  • DOI: 10.1016/j.jmb.2013.12.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitra ...

    Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitrate regulatory element (Nre) for transcriptional activation of genes involved in reduction and transport of nitrate and nitrite. Of the three proteins that constitute the Nre system, NreB has been characterized as an oxygen sensor kinase and NreC has been characterized as its cognate response regulator. Here, we present structural and functional data that establish NreA as a new type of nitrate receptor. The structure of NreA with bound nitrate was solved at 2.35Å resolution, revealing a GAF domain fold. Isothermal titration calorimetry experiments showed that NreA binds nitrate with low micromolar affinity (KD=22μM). Two crystal forms for NreA were obtained, with either bound nitrate or iodide. While the binding site is hydrophobic, two helix dipoles and polar interactions contribute to specific binding of the ions. The expression of nitrate reductase (NarGHI) was examined using a narG-lip (lipase) reporter gene assay in vivo. Expression was regulated by the presence of NreA and nitrate. Structure-guided mutations of NreA reduced its nitrate binding affinity and also affected the gene expression, thus providing support for the function of NreA as a nitrate receptor.


    Organizational Affiliation

    Interfaculty Institute of Biochemistry, Universität Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NreA protein
A, B
167Staphylococcus carnosus (strain TM300)Mutation(s): 0 
Gene Names: nreA
Find proteins for B9DL91 (Staphylococcus carnosus (strain TM300))
Go to UniProtKB:  B9DL91
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.660α = 90.00
b = 85.660β = 90.00
c = 91.340γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
BsxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2014-03-26
    Type: Database references