Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.5A resolution

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation.

Heikal, A.Nakatani, Y.Dunn, E.Weimar, M.R.Day, C.L.Baker, E.N.Lott, J.S.Sazanov, L.A.Cook, G.M.

(2014) Mol Microbiol 91: 950-964

  • DOI: https://doi.org/10.1111/mmi.12507
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5 Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors.

  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD-dependent pyridine nucleotide-disulfide oxidoreductase
A, B, C, D
405Caldalkalibacillus thermarum TA2.A1Mutation(s): 0 
Gene Names: CathTA2_0279
Find proteins for F5L3B8 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5L3B8 
Go to UniProtKB:  F5L3B8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5L3B8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.791α = 90
b = 114.477β = 92.04
c = 130.594γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Refinement description