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Enzyme Nomenclature
Information on EC 1.6.5.9 - NADH:ubiquinone reductase (non-electrogenic)
Word Map on EC 1.6.5.9
- 1.6.5.9
- lipolytica
-
single-subunit
-
rotenone-sensitive
-
cyanide-insensitive
- dichloroindophenol
-
beetroot
-
supercomplexes
- ubiquinone-1
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
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EC NUMBER 
COMMENTARY 
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
ORGANISM
UNIPROT
LITERATURE
NADH + H+ + ubiquinone = NAD+ + ubiquinol
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-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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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.
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CAS REGISTRY NUMBER
COMMENTARY
9028-04-0
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
genes ndeA-B and ndiA encoding external and internal alternative NADH dehydrogenases
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
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
malfunction
-
strains carrying the deletion of NDH2 are completely viable
malfunction
-
the induced RNAi cell line exhibits slower growth, decreased mitochondrial membrane potential and lower sensitivity of respiration to inhibitors. Mitochondrial membrane potential is altered in NDH2 knockdown. Growth phenotype of procyclic Trypanosoma brucei interfered against NDH2, overview
malfunction
-
the induced RNAi cell line exhibits slower growth, decreased mitochondrial membrane potential and lower sensitivity of respiration to inhibitors. Mitochondrial membrane potential is altered in NDH2 knockdown. Growth phenotype of procyclic Trypanosoma brucei interfered against NDH2, overview
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malfunction
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strains carrying the deletion of NDH2 are completely viable
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physiological function
-
isoform NDH2i allows survival of double mutants lacking both complex I and isoform NDH2e
physiological function
-
internal alternative NADH:ubiquinone oxidoreductase is the only enzyme capable of feeding NADH generated in the mitochondrial matrix into the respiratory chain
physiological function
-
NDH-II is a key enzyme for the regeneration of an oxidized form of NAD
physiological function
-
external rotenone-insensitive NADH:ubiquinone oxidoreductases (NDE1 and NDE2), and one internal rotenone-insensitive NADH:ubiquinone reductase (NDI1) are involved in farnesol resistance
physiological function
-
NDH2 is a part of the respiratory chain that does not pump protons across the inner membrane. NDH2 is the major NADH: ubiquinone oxidoreductase responsible for cytosolic and not for mitochondrial NAD+ regeneration in the mitochondrion of procyclic Trypanosoma brucei. thatNDH2is facing intermembrane space, rendering complex I responsible only for the regeneration of matrix NAD+. Ability of NDH2 to fully compensate for the loss of complex I. NDH2 is essential for the maintenance of mitochondrial membrane potential in procyclic Trypanosoma brucei
physiological function
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NDH-II is a key enzyme for the regeneration of an oxidized form of NAD
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physiological function
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NDH2 is a part of the respiratory chain that does not pump protons across the inner membrane. NDH2 is the major NADH: ubiquinone oxidoreductase responsible for cytosolic and not for mitochondrial NAD+ regeneration in the mitochondrion of procyclic Trypanosoma brucei. thatNDH2is facing intermembrane space, rendering complex I responsible only for the regeneration of matrix NAD+. Ability of NDH2 to fully compensate for the loss of complex I. NDH2 is essential for the maintenance of mitochondrial membrane potential in procyclic Trypanosoma brucei
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additional information
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targeted expression of Ndi1 in fly neurons significantly increases lifespan without compromising fertility or physical activity. Expression of the yeast Ndi1 gene in Drosophila mitochondria leads to an increase in respiratory chain activity, overview
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
additional information
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NdeA shows a pyridine nucleotide-disulfide oxidoreductase domain, a small NADH binding domain within a larger FAD binding domain at amino acid positions 226-334, and an EF-hand calcium-binding domain at amino acid positions 433-468
additional information
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Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, directed to the mitochondrial matrix. It is a peripheral membrane protein forming an intimate dimer, in which packing of the monomeric units within the dimer creates an amphiphilic membrane-anchor domain structure. Structures of the Ndi1NAD+ and Ndi1UQ2 complexes show overlapping binding sites for the NAD+ and quinone substrates
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
NADH + H+ + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
-
-
-
-
?
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
-
-
-
?
NADH + H+ + duroquinone
NAD+ + duroquinol
-
49% activity compared to ubiquinone-1
-
-
?
NADH + H+ + menadione
NAD+ + menadiol
-
47% activity compared to ubiquinone-1
-
-
?
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
-
-
-
?
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
-
-
-
?
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
-
-
-
?
2 ferricyanide + NADH
2 ferrocyanide + NAD+ + H+
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15% activity compared to ubiquinone-1
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-
?
NADH + H+ + 2,6-dichloroindophenol
NAD+ + reduced 2,6-dichloroindophenol
-
17% activity compared to ubiquinone-1
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-
?
NADH + H+ + 2,6-dichloroindophenol
NAD+ + reduced 2,6-dichloroindophenol
-
-
-
-
?
NADH + H+ + ubiquinone-2
NAD+ + ubiquinol-2
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ubiquinone is the best electron acceptor
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-
?
additional information
?
-
-
NDH-II does not pump protons
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-
-
additional information
?
-
-
the yeast enzyme is a two-electron reaction enzyme
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-
-
additional information
?
-
-
NAD+ binds in the second Rossmann domain in a predominantly positively charged cleft, with the nicotinamide ring approaching the re-face of the FAD
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-
-
additional information
?
-
-
the alternative NADH:ubiquinone oxidoreductase does not contribute to the proton gradient across the respiratory membrane
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-
-
additional information
?
-
-
alternative NADH:ubiquinone oxidoreductase does not pump protons across the inner mitochondrial membrane
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-
-
additional information
?
-
-
NDH2 does not translocate protons across the inner mitochondrial membrane
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-
-
additional information
?
-
NDH2e is a peripheral single-subunit oxido-reductase that does not pump protons
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-
-
additional information
?
-
-
alternative NADH:ubiquinone oxidoreductase does not pump protons across the inner mitochondrial membrane
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-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
the alternative NADH:ubiquinone oxidoreductase does not contribute to the proton gradient across the respiratory membrane
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-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FAD
-
the enzyme contains one molecule of noncovalently bound FAD as redox cofactor
FAD
-
binding site structure, overview. The isoalloxazine ring of the FAD is positioned between the two Rossmann domains, which define two channels along the interdomain plane that lead to the active site
NADH
-
the enzyme is specific for NADH. NADPH or deamino-NADH show rates that are at least 250times lower than obtained with NADH at any pH between 5.5 and 8.5
NADH
-
small NADH binding domain within a larger FAD binding domain at amino acid positions 226-334
additional information
-
the enzyme contains no iron-sulfur clusters
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additional information
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the mature enzyme contains no iron-sulfur clusters
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additional information
Ndi1 contains no iron-sulfur cluster
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additional information
-
the enzyme lacks iron-sulfur clusters
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
AMP
-
dead end reversible inhibitor, competitive inhibitor of NADH and uncompetitive inhibitor of 2,6-dichlorophenolindophenol
aurachin C 1-10
-
12% residual activity at 0.01 mM, noncompetitive inhibitor
rotenone
-
three NADH dehydrogenases, two external rotenone-insensitive NADH:ubiquinone oxidoreductases (NDE1 and NDE2), and one internal rotenone-insensitive NADH:ubiquinone reductase (NDI1)
scopafungin
-
33% residual activity at 0.005 mg/ml, noncompetitive inhibitor
additional information
-
the enzyme is not inhibited by rotenone, and activity is not affected by EDTA (1 mM), EGTA (1 mM) or Ca2+ or Mg2+ (1 mM)
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additional information
-
NADH oxidation is completely insensitive to amytal and rotenone
-
additional information
-
NAD+, Mg-ADP, Mg-ATP, Ca2+ (all at 2 mM) or piericidin, rotenone (both at 0.01 mM) or adenosyl-3'-O-[3-[N-(4-azido-2-nitrophenyl)-amino]propionyl]-NAD+ (0.05 mM) are without inhibitory or stimulatory effects
-
additional information
-
not inhibited by rotenone, NAD+ does not inhibit the activity of the enzyme, even at concentrations as high as 10 mM
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additional information
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not inhibited by piericidin A. Addition of up to 10% (v/v) ethanol has no effect on NADH:NBQ oxidoreductase activity
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
0.0152
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
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.031
NADH
Saccharomyces cerevisiae
-
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
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
11.5
AMP
-
linear uncompetitive inhibition of 2,6-dichlorophenolindophenol, pH 7.0, 25°C
0.0054
flavone
-
hyperbolic uncompetitive inhibition of NADH, pH 7.0, 25°C
0.0071
flavone
-
hyperbolic noncompetitive inhibition of 2,6-dichlorophenolindophenol, pH 7.0, 25°C
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0017
1-hydroxy-2-dodecyl-4(1H)quinolone
Gluconobacter oxydans
-
at 25°C in 100mM Tris-HCl (pH 7.4)
0.095
flavone
Saccharomyces cerevisiae
-
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
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.78
-
crude extract, using ubiquinone-2 as substrate, at pH 6.2, temperature not specified in the publication
61.9
-
after 2134fold purification, using ubiquinone-6 as substrate, at pH 6.2, temperature not specified in the publication
69.2
-
after 18.7fold purification, using ubiquinone-1 as substrate, at 25°C and pH 7.2
1671
-
after 2134fold purification, using ubiquinone-2 as substrate, at pH 6.2, temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.2
-
with ubiquinone-2 as acceptor a sharp maximum at pH 6.2 is obtained
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.5 - 9.5
-
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
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
NDH-II is bound peripherally to the inner surface of the cytoplasmic membrane
-
-
NDH-II is bound peripherally to the inner surface of the cytoplasmic membrane
-
-
-
Ndi1 is a peripheral membrane protein forming an intimate dimer, in which packing of the monomeric units within the dimer creates an amphiphilic membrane-anchor domain structure, membrane-anchor domain, overview
outer surface of the inner mitochondrial membrane
-
NDH2 is oriented towards the external face of the mitochondrial inner membrane
-
NDH2 is oriented towards the external face of the mitochondrial inner membrane
-
-
Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, directed to the matrix
-
after import, isoform NDA is intramitochondrially sorted to the matrix side of the inner membrane, whereas isoform NDB becomes exposed to the intermembrane space
-
after import, isoform NDA is intramitochondrially sorted to the matrix side of the inner membrane, whereas isoform NDB becomes exposed to the intermembrane space
-
-
alternative NADH dehydrogenase activity is located exclusively at the external face of the mitochondrial inner membrane
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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)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
33900
-
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
-
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
53000
55000
60000
55000
-
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
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
-
NDH-2 structure analysis by circular dichroism and Fourier transform infrared spectroscopy using the recombinanatly expressed enzyme and modelling, overview
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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
LITERATURE
5.5 - 8
-
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
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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
DEAE Bio-gel column chromatography and Blue Sepharose CL-6B column chromatography, column chromatography
-
DEAE-cellulose column chromatography and blue Sepharose CL-6B column chromatography
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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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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
LITERATURE
additional information
additional information
-
when exposed to farnesol, the DELTAaifA and DELTAndeA strains have increased reactive oxygen species production while DndeB, DELTAndeA DELTAndeB, and DELTAndiA mutant strains show the same reactive oxygen species accumulation than in the absence of farnesol
additional information
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NDH2 gene silencing using tetracycline-inducible RNAi
additional information
-
NDH2 gene silencing using tetracycline-inducible RNAi
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LINKS TO OTHER DATABASES (specific for EC-Number 1.6.5.9)
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