5JEF

Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in asymmetric holo state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanism of transmembrane signaling by sensor histidine kinases.

Gushchin, I.Melnikov, I.Polovinkin, V.Ishchenko, A.Yuzhakova, A.Buslaev, P.Bourenkov, G.Grudinin, S.Round, E.Balandin, T.Borshchevskiy, V.Willbold, D.Leonard, G.Buldt, G.Popov, A.Gordeliy, V.

(2017) Science 356

  • DOI: https://doi.org/10.1126/science.aah6345
  • Primary Citation of Related Structures:  
    5IJI, 5JEF, 5JEQ

  • PubMed Abstract: 

    One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. We present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor histidine kinase NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces rearrangements and pistonlike shifts of TM helices. The HAMP domain protomers undergo leverlike motions and convert these pistonlike motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCSs.


  • Organizational Affiliation

    Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany. ivan.gushchin@phystech.edu valentin.gordeliy@ibs.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrate/nitrite sensor protein NarQ
A, B
236Escherichia coli K-12Mutation(s): 0 
Gene Names: narQb2469JW2453
EC: 2.7.13.3
Membrane Entity: Yes 
UniProt
Find proteins for P27896 (Escherichia coli (strain K12))
Explore P27896 
Go to UniProtKB:  P27896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27896
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LFA
Query on LFA

Download Ideal Coordinates CCD File 
D [auth A]EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.464α = 90
b = 39.865β = 100.62
c = 120.361γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description