5ER0 | pdb_00005er0

Water-forming NADH oxidase from Lactobacillus brevis (LbNOX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio.

Titov, D.V.Cracan, V.Goodman, R.P.Peng, J.Grabarek, Z.Mootha, V.K.

(2016) Science 352: 231-235

  • DOI: https://doi.org/10.1126/science.aad4017
  • Primary Citation Related Structures: 
    5ER0

  • PubMed Abstract: 

    A decline in electron transport chain (ETC) activity is associated with many human diseases. Although diminished mitochondrial adenosine triphosphate production is recognized as a source of pathology, the contribution of the associated reduction in the ratio of the amount of oxidized nicotinamide adenine dinucleotide (NAD(+)) to that of its reduced form (NADH) is less clear. We used a water-forming NADH oxidase from Lactobacillus brevis (LbNOX) as a genetic tool for inducing a compartment-specific increase of the NAD(+)/NADH ratio in human cells. We used LbNOX to demonstrate the dependence of key metabolic fluxes, gluconeogenesis, and signaling on the cytosolic or mitochondrial NAD(+)/NADH ratios. Expression of LbNOX in the cytosol or mitochondria ameliorated proliferative and metabolic defects caused by an impaired ETC. The results underscore the role of reductive stress in mitochondrial pathogenesis and demonstrate the utility of targeted LbNOX for direct, compartment-specific manipulation of redox state.


  • Organizational Affiliation
    • Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. Department of Systems Biology, Harvard Medical School, Boston, MA, USA. Broad Institute, Cambridge, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 228.53 kDa 
  • Atom Count: 14,950 
  • Modeled Residue Count: 1,800 
  • Deposited Residue Count: 2,072 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH oxidase
A, B, C, D
518Levilactobacillus brevisMutation(s): 0 
UniProt
Find proteins for Q03Q85 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03Q85 
Go to UniProtKB:  Q03Q85
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03Q85
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
P [auth C],
S [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
OXY

Query on OXY



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B],
Q [auth C],
T [auth D]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.968α = 96.92
b = 86.35β = 94.07
c = 93.327γ = 92.4
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099683

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description