Water-forming NADH oxidase from Lactobacillus brevis (LbNOX) bound to NADH.

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


A genetically encoded tool for manipulation of NADP(+)/NADPH in living cells.

Cracan, V.Titov, D.V.Shen, H.Grabarek, Z.Mootha, V.K.

(2017) Nat Chem Biol 13: 1088-1095

  • DOI: https://doi.org/10.1038/nchembio.2454
  • Primary Citation of Related Structures:  
    5VN0, 5VOH

  • PubMed Abstract: 

    The redox coenzymes NADH and NADPH are broadly required for energy metabolism, biosynthesis and detoxification. Despite detailed knowledge of specific enzymes and pathways that utilize these coenzymes, a holistic understanding of the regulation and compartmentalization of NADH- and NADPH-dependent pathways is lacking, partly because of a lack of tools with which to investigate these processes in living cells. We have previously reported the use of the naturally occurring Lactobacillus brevis H 2 O-forming NADH oxidase (LbNOX) as a genetic tool for manipulation of the NAD + /NADH ratio in human cells. Here, we present triphosphopyridine nucleotide oxidase (TPNOX), a rationally designed and engineered mutant of LbNOX that is strictly specific to NADPH. We characterized the effects of TPNOX expression on cellular metabolism and used it in combination with LbNOX to show how the redox states of mitochondrial NADPH and NADH pools are connected.

  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(FAD)-dependent dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
518Levilactobacillus brevis ATCC 367Mutation(s): 0 
Gene Names: LVIS_1558
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
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
I [auth A]
KA [auth G]
N [auth B]
AA [auth E],
EA [auth F],
I [auth A],
KA [auth G],
N [auth B],
OA [auth H],
R [auth C],
V [auth D]
C27 H33 N9 O15 P2
Query on NAI

Download Ideal Coordinates CCD File 
CA [auth E]
GA [auth F]
K [auth A]
MA [auth G]
P [auth B]
CA [auth E],
GA [auth F],
K [auth A],
MA [auth G],
P [auth B],
QA [auth H],
T [auth C],
X [auth D]
C21 H29 N7 O14 P2
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth E]
HA [auth F]
IA [auth F]
JA [auth F]
L [auth A]
DA [auth E],
HA [auth F],
IA [auth F],
JA [auth F],
L [auth A],
M [auth A],
NA [auth G],
Q [auth B],
RA [auth H],
SA [auth H],
U [auth C],
Y [auth D],
Z [auth D]
C2 H6 O2
Query on OXY

Download Ideal Coordinates CCD File 
BA [auth E]
FA [auth F]
J [auth A]
LA [auth G]
O [auth B]
BA [auth E],
FA [auth F],
J [auth A],
LA [auth G],
O [auth B],
PA [auth H],
S [auth C],
W [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.525α = 63.37
b = 107.511β = 90.04
c = 119.298γ = 89.95
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

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 StatesR01GM099683

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references, Refinement description
  • Version 1.2: 2017-09-27
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description