4FC4

FNT family ion channel

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural and functional characterization of the nitrite channel NirC from Salmonella typhimurium.

Lu, W., Schwarzer, N.J., Du, J., Gerbig-Smentek, E., Andrade, S.L., Einsle, O.

(2012) Proc.Natl.Acad.Sci.USA 109: 18395-18400

  • DOI: 10.1073/pnas.1210793109

  • PubMed Abstract: 

    • Nitrite (NO(2)(-)) is a central intermediate in the nitrogen metabolism of microorganisms and plants, and is used as a cytotoxin by macrophages as part of the innate immune response. The bacterial membrane protein NirC acts as a specific channel to f ...

    Nitrite (NO(2)(-)) is a central intermediate in the nitrogen metabolism of microorganisms and plants, and is used as a cytotoxin by macrophages as part of the innate immune response. The bacterial membrane protein NirC acts as a specific channel to facilitate the transport of nitrite anions across lipid bilayers for cytoplasmic detoxification. Despite NirC's importance in nitrogen metabolism and in the pathogenicity of enteric bacteria, available biochemical data are scarce. Here we present a functional and structural characterization of NirC from Salmonella typhimurium by lipid bilayer electrophysiology and X-ray crystallography. NirC is a pentameric member of the formate/nitrite transporter family of membrane proteins that operates as a channel with high conductance. Single-channel measurements reveal fast and slow gating events but, in contrast to the related FocA formate channel, no pH-dependent gating. A 2.4Å crystal structure of NirC at pH 5 shows similarity to FocA and aquaporins, but lacks the structural asymmetry observed in the formate channel at similarly low pH. Resolved water molecules in the protomers suggest a transport mechanism that also permits a facultative NO(2)(-)/H(+) symport.

    Organizational Affiliation: 

    Lehrstuhl für Biochemie, Institut für organische Chemie und Biochemie and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrite transporter NirC
A, B, C, D, E, F, G, H, I, J
261Salmonella typhimurium (strain 4/74)Mutation(s): 0 
Gene Names: nirC
Find proteins for E8XEH9 (Salmonella typhimurium (strain 4/74))
Go to UniProtKB:  E8XEH9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG
Download SDF File 
Download CCD File 
F
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 176.300α = 90.00
b = 101.840β = 101.24
c = 205.300γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XPREPdata reduction
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary