4U4V

Structure of a nitrate/nitrite antiporter NarK in apo inward-open state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK

Fukuda, M.Takeda, H.Kato, H.E.Doki, S.Ito, K.Maturana, A.D.Ishitani, R.Nureki, O.

(2015) Nat Commun 6: 7097-7097

  • DOI: 10.1038/ncomms8097
  • Primary Citation of Related Structures:  
    4U4T, 4U4V, 4U4W

  • PubMed Abstract: 
  • NarK belongs to the nitrate/nitrite porter (NNP) family in the major facilitator superfamily (MFS) and plays a central role in nitrate uptake across the membrane in diverse organisms, including archaea, bacteria, fungi and plants. Although previous s ...

    NarK belongs to the nitrate/nitrite porter (NNP) family in the major facilitator superfamily (MFS) and plays a central role in nitrate uptake across the membrane in diverse organisms, including archaea, bacteria, fungi and plants. Although previous studies provided insight into the overall structure and the substrate recognition of NarK, its molecular mechanism, including the driving force for nitrate transport, remained elusive. Here we demonstrate that NarK is a nitrate/nitrite antiporter, using an in vitro reconstituted system. Furthermore, we present the high-resolution crystal structures of NarK from Escherichia coli in the nitrate-bound occluded, nitrate-bound inward-open and apo inward-open states. The integrated structural, functional and computational analyses reveal the nitrate/nitrite antiport mechanism of NarK, in which substrate recognition is coupled to the transport cycle by the concomitant movement of the transmembrane helices and the key tyrosine and arginine residues in the substrate-binding site.


    Organizational Affiliation

    1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrate/nitrite transporter NarKA475Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: narKb1223JW1214
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
NarK nitrate/nitrite exchanger, apo inward-open
Find proteins for P10903 (Escherichia coli (strain K12))
Explore P10903 
Go to UniProtKB:  P10903
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.504α = 90
b = 106.532β = 90
c = 124.609γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Derived calculations, Source and taxonomy