6FWF

Low resolution structure of Neisseria meningitidis qNOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.373 
  • R-Value Work: 0.333 
  • R-Value Observed: 0.335 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme.

Gonska, N.Young, D.Yuki, R.Okamoto, T.Hisano, T.Antonyuk, S.Hasnain, S.S.Muramoto, K.Shiro, Y.Tosha, T.Adelroth, P.

(2018) Sci Rep 8: 3637

  • DOI: https://doi.org/10.1038/s41598-018-21804-0
  • Primary Citation of Related Structures:  
    6FWF

  • PubMed Abstract: 

    Bacterial nitric oxide reductases (NORs) catalyse the reduction of NO to N 2 O and H 2 O. NORs are found either in denitrification chains, or in pathogens where their primary role is detoxification of NO produced by the immune defense of the host. Although NORs belong to the heme-copper oxidase superfamily, comprising proton-pumping O 2 -reducing enzymes, the best studied NORs, cNORs (cytochrome c-dependent), are non-electrogenic. Here, we focus on another type of NOR, qNOR (quinol-dependent). Recombinant qNOR from Neisseria meningitidis, a human pathogen, purified from Escherichia coli, showed high catalytic activity and spectroscopic properties largely similar to cNORs. However, in contrast to cNOR, liposome-reconstituted qNOR showed respiratory control ratios above two, indicating that NO reduction by qNOR was electrogenic. Further, we determined a 4.5 Å crystal structure of the N. meningitidis qNOR, allowing exploration of a potential proton transfer pathway from the cytoplasm by mutagenesis. Most mutations had little effect on the activity, however the E-498 variants were largely inactive, while the corresponding substitution in cNOR was previously shown not to induce significant effects. We thus suggest that, contrary to cNOR, the N. meningitidis qNOR uses cytoplasmic protons for NO reduction. Our results allow possible routes for protons to be discussed.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric-oxide reductase751Neisseria meningitidis alpha14Mutation(s): 0 
Gene Names: norBNMO_1451
EC: 1.7.99.7
Membrane Entity: Yes 
UniProt
Find proteins for C6S880 (Neisseria meningitidis (strain alpha14))
Explore C6S880 
Go to UniProtKB:  C6S880
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6S880
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.373 
  • R-Value Work: 0.333 
  • R-Value Observed: 0.335 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.682α = 90
b = 123.096β = 90
c = 130.845γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description