4NWZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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: 10.1111/mmi.12507
  • Primary Citation of Related Structures:  
    4NWZ

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAD-dependent pyridine nucleotide-disulfide oxidoreductaseA, B, C, D405Caldalkalibacillus thermarum TA2.A1Mutation(s): 0 
Gene Names: CathTA2_0279
UniProt
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
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 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 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
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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