5KMP

The structure of G164E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The mechanism of catalysis by type-II NADH:quinone oxidoreductases.

Blaza, J.N.Bridges, H.R.Aragao, D.Dunn, E.A.Heikal, A.Cook, G.M.Nakatani, Y.Hirst, J.

(2017) Sci Rep 7: 40165-40165

  • DOI: 10.1038/srep40165
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in ne ...

    Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies.


    Organizational Affiliation

    MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAD-dependent pyridine nucleotide-disulfide oxidoreductase
A, B
405Caldalkalibacillus thermarum (strain TA2.A1)Mutation(s): 1 
Find proteins for F5L3B8 (Caldalkalibacillus thermarum (strain TA2.A1))
Go to UniProtKB:  F5L3B8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.098α = 90.00
b = 93.098β = 90.00
c = 248.483γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release