Information on EC 1.6.5.9 - NADH:ubiquinone reductase (non-electrogenic)

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.6.5.9
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RECOMMENDED NAME
GeneOntology No.
NADH:ubiquinone reductase (non-electrogenic)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
NADH + H+ + ubiquinone = NAD+ + ubiquinol
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
aerobic respiration II (cytochrome c) (yeast)
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NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast)
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NADH to cytochrome bd oxidase electron transfer II
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NADH to cytochrome bo oxidase electron transfer II
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nitrate reduction VIIIb (dissimilatory)
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SYSTEMATIC NAME
IUBMB Comments
NADH:ubiquinone oxidoreductase
A flavoprotein (FAD). Occurs in mitochondria of yeast and plants, and in aerobic bacteria. Has low activity with NADPH.
CAS REGISTRY NUMBER
COMMENTARY hide
9028-04-0
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
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Manually annotated by BRENDA team
genes ndeA-B and ndiA encoding external and internal alternative NADH dehydrogenases
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
formerly Gluconobacter suboxydans strain IFO12528
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Manually annotated by BRENDA team
formerly Gluconobacter suboxydans strain IFO12528
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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three NADH dehydrogenases, two external rotenone-insensitive NADH:ubiquinone oxidoreductases (NDE1 and NDE2), and one internal rotenone-insensitive NADH:ubiquinone reductase (NDI1)
malfunction
metabolism
NDH2e-derived electrons are channelled to the cytochrome pathway
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2 ferricyanide + NADH
2 ferrocyanide + NAD+ + H+
show the reaction diagram
NADH + H+ + 2,6-dichloroindophenol
NAD+ + reduced 2,6-dichloroindophenol
show the reaction diagram
NADH + H+ + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + H+ + 2-azido-5-geranyl-3-methoxy-6-methyl-1,4-benzoquinone
NAD+ + 2-azido-5-geranyl-3-methoxy-6-methyl-1,4-benzoquinol
show the reaction diagram
-
-
-
?
NADH + H+ + 5-nonylubiquinone
NAD+ + 5-nonylubiquinol
show the reaction diagram
NADH + H+ + duroquinone
NAD+ + duroquinol
show the reaction diagram
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49% activity compared to ubiquinone-1
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?
NADH + H+ + juglone
NAD+ + ?
show the reaction diagram
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29% activity compared to ubiquinone-1
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?
NADH + H+ + menadione
NAD+ + menadiol
show the reaction diagram
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47% activity compared to ubiquinone-1
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?
NADH + H+ + menaquinone
NAD+ + menaquinol
show the reaction diagram
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-
-
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?
NADH + H+ + N-(6-[[(4E,8E)-10-(4-azido-5-methoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]amino]-6-oxohexyl)-6-([5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl]amino)hexanamide
NAD+ + N-(6-[[(4E,8E)-10-(4-azido-3,6-dihydroxy-5-methoxy-2-methylcyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]amino]-6-oxohexyl)-6-([5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl]amino)hexanamide
show the reaction diagram
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-
-
?
NADH + H+ + n-decylubiquinone
NAD+ + n-decylubiquinol
show the reaction diagram
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-
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?
NADH + H+ + N-[(4E,8E)-10-(4-azido-5-methoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]-6-([5-[(3aS,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl]amino)hexanamide
NAD+ + N-[(4E,8E)-10-(4-azido-3,6-dihydroxy-5-methoxy-2-methylcyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]-6-([5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl]amino)hexanamide
show the reaction diagram
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?
NADH + H+ + N-[2-[2-(2-[[(4E,8E)-10-(4-azido-5-methoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]oxy]ethoxy)ethoxy]ethyl]-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide
NAD+ + N-[2-[2-(2-[[(4E,8E)-10-(4-azido-3,6-dihydroxy-5-methoxy-2-methylcyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]oxy]ethoxy)ethoxy]ethyl]-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide
show the reaction diagram
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?
NADH + H+ + ubiquinone
NAD+ + ubiquinol
show the reaction diagram
NADH + H+ + ubiquinone-1
NAD+ + ubiquinol-1
show the reaction diagram
NADH + H+ + ubiquinone-10
NAD+ + ubiquinol-10
show the reaction diagram
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-
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?
NADH + H+ + ubiquinone-2
NAD+ + ubiquinol-2
show the reaction diagram
NADH + H+ + ubiquinone-6
NAD+ + ubiquinol-6
show the reaction diagram
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
NADH + H+ + ubiquinone
NAD+ + ubiquinol
show the reaction diagram
additional information
?
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the alternative NADH:ubiquinone oxidoreductase does not contribute to the proton gradient across the respiratory membrane
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADPH
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below pH 7.0 NADPH is slowly oxidized
additional information
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-hydroxy-2-dodecyl-4(1H)quinolone
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28% residual activity at 0.01 mM
2,6-dichlorophenolindophenol
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substrate inhibition
aculeacin A
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63% residual activity at 0.005 mg/ml
AMP
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dead end reversible inhibitor, competitive inhibitor of NADH and uncompetitive inhibitor of 2,6-dichlorophenolindophenol
aurachin analogue AC0-10
specific inhibitor
aurachin C 1-10
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12% residual activity at 0.01 mM, noncompetitive inhibitor
flavone
funiculosin
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68% residual activity at 0.005 mg/ml
Gramicidin S
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31% residual activity at 0.005 mg/ml
NADH
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substrate inhibition
polymixin B
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51% residual activity at 0.005 mg/ml
reduced 2,6-dichlorophenolindophenol
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product inhibition
rotenone
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three NADH dehydrogenases, two external rotenone-insensitive NADH:ubiquinone oxidoreductases (NDE1 and NDE2), and one internal rotenone-insensitive NADH:ubiquinone reductase (NDI1)
scopafungin
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33% residual activity at 0.005 mg/ml, noncompetitive inhibitor
staurosporine
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70% residual activity at 0.005 mg/ml
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0062
2,6-dichlorophenolindophenol
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pH 7.0, 25°C
0.0181
N-(6-[[(4E,8E)-10-(4-azido-5-methoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]amino]-6-oxohexyl)-6-([5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl]amino)hexanamide
in 50 mM sodium phosphate buffer (pH 6.0) and 1 mM EDTA, temperature not specified in the publication
0.022
N-[(4E,8E)-10-(4-azido-5-methoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]-6-([5-[(3aS,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl]amino)hexanamide
in 50 mM sodium phosphate buffer (pH 6.0) and 1 mM EDTA, temperature not specified in the publication
0.033
N-[2-[2-(2-[[(4E,8E)-10-(4-azido-5-methoxy-2-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl)-4,8-dimethyldeca-4,8-dien-1-yl]oxy]ethoxy)ethoxy]ethyl]-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide
in 50 mM sodium phosphate buffer (pH 6.0) and 1 mM EDTA, temperature not specified in the publication
0.0094 - 0.157
NADH
0.0152
ubiquinone-1
in 50 mM sodium phosphate buffer (pH 6.0) and 1 mM EDTA, temperature not specified in the publication
0.0079
ubiquinone-2
in 50 mM sodium phosphate buffer (pH 6.0) and 1 mM EDTA, temperature not specified in the publication
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.031
NADH
Saccharomyces cerevisiae
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using ubiquinone-2 as substrate, in 20 mM MOPS/KOH, 1 mM EDTA, 0.03% (v/v) Triton X-100, 200 mM KCl, pH 6.2, temperature not specified in the publication
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1152
2,6-dichlorophenolindophenol
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pH 7.0, 25°C
5.5 - 11.5
AMP
0.0054 - 0.0071
flavone
0.0014
Gramicidin S
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at 25°C in 100mM Tris-HCl (pH 7.4)
0.0525
NADH
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pH 7.0, 25°C
0.0141
reduced 2,6-dichlorophenolindophenol
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pH 7.0, 25°C
0.0055
scopafungin
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at 25°C in 100mM Tris-HCl (pH 7.4)
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0017
1-hydroxy-2-dodecyl-4(1H)quinolone
Gluconobacter oxydans
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at 25°C in 100mM Tris-HCl (pH 7.4)
0.00034
aurachin C 1-10
Gluconobacter oxydans
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at 25°C in 100mM Tris-HCl (pH 7.4)
0.095 - 0.175
flavone
0.0012
Gramicidin S
Gluconobacter oxydans
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at 25°C in 100mM Tris-HCl (pH 7.4)
0.0062
scopafungin
Gluconobacter oxydans
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at 25°C in 100mM Tris-HCl (pH 7.4)
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.78
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crude extract, using ubiquinone-2 as substrate, at pH 6.2, temperature not specified in the publication
3.7
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crude enzyme, using ubiquinone-1 as substrate, at 25°C and pH 7.2
61.9
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after 2134fold purification, using ubiquinone-6 as substrate, at pH 6.2, temperature not specified in the publication
69.2
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after 18.7fold purification, using ubiquinone-1 as substrate, at 25°C and pH 7.2
1671
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after 2134fold purification, using ubiquinone-2 as substrate, at pH 6.2, temperature not specified in the publication
3372
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crude enzyme, using ubiquinone-1 as substrate, at 25°C and pH 7.2
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.2
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with ubiquinone-2 as acceptor a sharp maximum at pH 6.2 is obtained
7.2
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pH-optimum around pH 7.2
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5 - 9.5
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with ubiquinone-6 as acceptor the activity is almost constant between pH 4.5 and 9.5, at pH values lower than 4.5 and higher than 9.5, enzymic activity is irreversibly destroyed
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5
native enzyme, calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
33900
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the rotenone-insensitive NADH-ubiquinone-1 reductase activity eluted by 0.5 M NaCl displays three major bands on SDS-PAGE of 55000, 39200 and 33900 Da
39200
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the rotenone-insensitive NADH-ubiquinone-1 reductase activity eluted by 0.5 M NaCl displays three major bands on SDS-PAGE of 55000, 39200 and 33900 Da
52000
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isoform NDA, SDS-PAGE
65000
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isoform NDB, calculated from amino acid sequence
65800
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calculated from amino acid sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
additional information
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NDH-2 structure analysis by circular dichroism and Fourier transform infrared spectroscopy using the recombinanatly expressed enzyme and modelling, overview
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ndi1 in its substrate-free, NAD+- and ubiquinone-complexed states, X-ray diffraction structure determination and analysis
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 8
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the free enzyme and the binary complex E-NADH are highly stable in the pH range from 5.5 to 8.0, maintaining the initial activity after 10 min incubation. Maximal stability is observed at pH 5.0 and 6.5 with no loss in activity. The enzyme is highly unstable above and below this pH range
392700
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is stable at low protein concentrations and in the presence of both substrates
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
5'-ADP-Sepharose 4B column chromatography
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DEAE Bio-gel column chromatography and Blue Sepharose CL-6B column chromatography, column chromatography
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DEAE-cellulose column chromatography and blue Sepharose CL-6B column chromatography
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DEAE-Sepharose column chromatography
recombinant His-tagged NDH-2 by nickel affinity chromatography
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streptavidin-agarose chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) pLysS cells
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expressed in Escherichia coli BL21(DE3)pLysS cells
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expressed in Escherichia coli membranes
gene Ndi1, inducible NDI1 enzyme expression in Drosophila melanogaster mitochondria of different cells and tissues. Expression of Ndi1 in fly mitochondria leads to an increase in NADH-ubiquinone oxidoreductase activity, oxygen consumption and ATP levels. In addition, exogenous Ndi1 expression results in increased CO2 production in living flies. Targeted expression of Ndi1 in fly neurons significantly increases lifespan without compromising fertility or physical activity
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recombinant expression of His-tagged NDH-2
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the amount of enzyme in the cell is subject to glucose repression, it increases slightly when cells, grown on glucose or lactate, enter the stationary phase
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information