5KMQ

The structure of I379E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report



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:  
    5KMP, 5KMR, 5KMQ, 5KMS

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAD-dependent pyridine nucleotide-disulfide oxidoreductaseA, B, C, D405Caldalkalibacillus thermarum TA2.A1Mutation(s): 1 
Gene Names: CathTA2_0279
Find proteins for F5L3B8 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5L3B8 
Go to UniProtKB:  F5L3B8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.383α = 90
b = 114.366β = 92.04
c = 130.462γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Health Research Council and Maurice Wilkins CentreNew Zealand--

Revision History 

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