Information on EC 1.6.99.3 - NADH dehydrogenase

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

EC NUMBER
COMMENTARY
1.6.99.3
-
RECOMMENDED NAME
GeneOntology No.
NADH dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
NADH + H+ + acceptor = NAD+ + reduced acceptor
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
oxidation
-
-
-
-
oxidation
P26829
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Metabolic pathways
-
Oxidative phosphorylation
-
SYSTEMATIC NAME
IUBMB Comments
NADH:acceptor oxidoreductase
A flavoprotein containing iron-sulfur centres. After preparations have been subjected to certain treatments, cytochrome c may act as an acceptor. Under normal conditions, two protons are extruded from the cytoplasm or the intramitochondrial or stromal compartment. Present in a mitochondrial complex as EC 1.6.5.3, NADH dehydrogenase (ubiquinone).
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Alkyl hydroperoxide reductase
-
-
-
-
beta-NADH dehydrogenase
-
-
-
-
cytochrome c reductase
-
-
-
-
dehydrogenase, reduced nicotinamide adenine dinucleotide
-
-
-
-
diaphorase
-
-
-
-
dihydrocodehydrogenase I dehydrogenase
-
-
-
-
dihydronicotinamide adenine dinucleotide dehydrogenase
-
-
-
-
diphosphopyridine diaphorase
-
-
-
-
DPNH dehydrogenase
-
-
-
-
DPNH diaphorase
-
-
-
-
EC 1.6.2.1
-
-
formerly
-
H(2)O(2) forming NADH oxidase
-
-
-
-
NADH dehydrogenase
-
-
NADH dehydrogenase I
-
-
NADH dehydrogenase-like complex
Synechocystis sp. PCC6803
-
-
-
NADH dehydrogenase-like complex
-
-
NADH diaphorase
-
-
-
-
NADH hydrogenase
-
-
-
-
NADH oxidoreductase
-
-
-
-
NADH-menadione oxidoreductase
-
-
-
-
NADH:oxygen oxidoreductase
-
-
-
-
NDH
Synechocystis sp. PCC6803
-
-
-
NDH
-
-
NDH-1
Synechocystis sp. PCC6803
-
-
-
NOXase
-
-
-
-
proteins, specific or class, gene MURF3
-
-
-
-
reduced diphosphopyridine nucleotide diaphorase
-
-
-
-
type I dehydrogenase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9079-67-8
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
strain YN-1
Uniprot
Manually annotated by BRENDA team
Bacillus subtilis W23
W23
-
-
Manually annotated by BRENDA team
strain PAO1, genes nuoD, nuoG, nuoM encoding components of the NADH dehydrogenase complex
-
-
Manually annotated by BRENDA team
Synechocystis sp. PCC6803
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
evolution
-
chloroplast and cyanobacterial NDHs have an electron donor-binding subcomplex that is unique to oxygenic photosynthetic organisms, backbone structure of NDH complex common in cyanobacteria and chloroplasts compared to NDH-1 in membranes in heterotrophic bacteria
physiological function
-
the chloroplast NADH dehydrogenase-like complex shows similarity to complex I in respiratory electron transport, and is involved in electron transport from photoproduced stromal reductants such as NADPH and ferredoxin to the intersystem plastoquinone pool. Chloroplast NDH may also be involved in the electron transport from stromal reductants to oxygen in chlororesipiration. Photosynthetic NDH apparently lacks subunits involved in electron input
physiological function
Synechocystis sp. PCC6803
-
the chloroplast NADH dehydrogenase-like complex shows similarity to complex I in respiratory electron transport, and is involved in electron transport from photoproduced stromal reductants such as NADPH and ferredoxin to the intersystem plastoquinone pool. Chloroplast NDH may also be involved in the electron transport from stromal reductants to oxygen in chlororesipiration. Photosynthetic NDH apparently lacks subunits involved in electron input
-
evolution
Synechocystis sp. PCC6803
-
chloroplast and cyanobacterial NDHs have an electron donor-binding subcomplex that is unique to oxygenic photosynthetic organisms, backbone structure of NDH complex common in cyanobacteria and chloroplasts compared to NDH-1 in membranes in heterotrophic bacteria
-
additional information
-
backbone structure of NDH complex, overview. Subcomplex structure of flowering plant NDH with specific subunits, four distinct subcomplexes: A, B, membrane-localized and lumen-localized subcomplexes. Dependence of the accumulation of nuclear-encoded NdhM-NdhO on that of NdhH-NdhL, and vice versa
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
?
NADH + 2,6-dichlorophenolindophenol
NAD+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
specific for NADH
-
-
-
NADH + 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
NAD+ + ?
show the reaction diagram
-
-
-
-
?
NADH + 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
NAD+ + ?
show the reaction diagram
-
-
-
-
?
NADH + 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
NAD+ + ?
show the reaction diagram
Bacillus subtilis W23
-
-
-
-
?
NADH + benzyl viologen
NAD+ + reduced benzyl viologen
show the reaction diagram
-
-
-
-
?
NADH + ferricyanide
NAD+ + ferrocyanide
show the reaction diagram
-
-
-
-
?
NADH + ferricyanide
NAD+ + ferrocyanide
show the reaction diagram
-
-
-
-
?
NADH + ferricyanide
NAD+ + ferrocyanide
show the reaction diagram
-
-
-
-
?
NADH + ferricyanide
NAD+ + ferrocyanide
show the reaction diagram
-
-
-
-
?
NADH + ferricyanide
NAD+ + ferrocyanide
show the reaction diagram
-
-
-
-
?
NADH + ferricyanide
NAD+ + ferrocyanide
show the reaction diagram
-
-
-
-
?
NADH + ferricyanide
NAD+ + ferrocyanide
show the reaction diagram
-
-
-
-
?
NADH + ferricytochrome b5
NAD+ + ferrocytochrome b5
show the reaction diagram
-
-
-
-
?
NADH + ferricytochrome b5
NAD+ + ferrocytochrome b5
show the reaction diagram
-
-
-
-
?
NADH + ferricytochrome c
NAD+ + ferrocytochrome c
show the reaction diagram
-
-
-
-
?
NADH + ferricytochrome c
NAD+ + ferrocytochrome c
show the reaction diagram
-
-
-
-
?
NADH + ferricytochrome c
NAD+ + ferrocytochrome c
show the reaction diagram
-
-
-
-
?
NADH + ferricytochrome c
NAD+ + ferrocytochrome c
show the reaction diagram
-
-
-
-
?
NADH + methemoglobin-ferrocyanide complex
NAD+ + ?
show the reaction diagram
-
-
-
-
?
NADH + methyl viologen
NAD+ + reduced methyl viologen
show the reaction diagram
-
-
-
-
?
NADPH + 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
NADP+ + ?
show the reaction diagram
-
less than 6% of the activity with NADH
-
-
?
NADPH + 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
NADP+ + ?
show the reaction diagram
-
rate of oxidation is less than 5% of the reaction with NADH
-
-
?
NADPH + 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
NADP+ + ?
show the reaction diagram
Bacillus subtilis W23
-
less than 6% of the activity with NADH
-
-
?
NADPH + H+ + 2,6-dichlorophenolindophenol
NADP+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
activity with NADPH is about 35% of the activity with NADH
-
-
?
NADPH + H+ + 2,6-dichlorophenolindophenol
NADP+ + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
less active as NADH
-
-
?
oxidized ferredoxin + NADH + H+
reduced ferredoxin + NAD+
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
the enzyme transfers electrons from NADH to external oxidants like ferricyanide through pathways which are linked to metabolic processess in the cell
-
-
-
additional information
?
-
-
the enzyme is localized at the main point of electron entry into the respiratory chain. The enzyme catalyzes the transfer of electrons from NADH to the respiratory electron transport components and hence links the major catabolic and energy-producing pathways
-
-
-
additional information
?
-
-
the enzyme also shows NADH oxidase activity
-
-
-
additional information
?
-
-
with anaerobic NO2-, the most downregulated genes are those involved postglycolytically and include many tricarboxylic acid cycle genes and those involved in the electron transport chain, especially those encoding the NADH dehydrogenase I complex, overview
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
the enzyme transfers electrons from NADH to external oxidants like ferricyanide through pathways which are linked to metabolic processess in the cell
-
-
-
additional information
?
-
-
the enzyme is localized at the main point of electron entry into the respiratory chain. The enzyme catalyzes the transfer of electrons from NADH to the respiratory electron transport components and hence links the major catabolic and energy-producing pathways
-
-
-
additional information
?
-
-
with anaerobic NO2-, the most downregulated genes are those involved postglycolytically and include many tricarboxylic acid cycle genes and those involved in the electron transport chain, especially those encoding the NADH dehydrogenase I complex, overview
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
FAD
-
contains one mol FAD per 36000 Da subunit
FAD
-
contains 1 molecule FAD per molecule
FAD
-
natural prosthetic group of the enzyme, apoenzyme catalyzed reaction with ferricyanide, FAD is required for reaction with 2,6-dichlorophenol or with cytochrome c, Km: 0.00056 mM
FMN
-
is about 10% as effective as FAD
NADH
-
specific for NADH
NADH
-
specific for NADH
NADPH
-
activity with NADPH is about 35% of the activity with NADH
NADPH
-
less active than NADH
NADPH
-
less than 6% of the activity with NADH in reaction with 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
NADPH
-
oxidized at about 5% the rate of NADH
additional information
-
no flavin detectable
-
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Acrinol
-
1 mM, complete inhibition
adenosine
-
slight inhibition
ADP
-
strong competitive
AMP
-
; 10 mM, 41% inhibition
Atebrin
-
1 mM, complete inhibition
ATP
-
10 mM, 17% inhibition
deoxyadenosine
-
slight inhibition
EDTA
-
10 mM, 21% inhibition
ferricyanide
-
competitive substrate inhibition due to its direct binding to the enzyme and forming an inactive binary complex
ferrocyanide
-
-
HgCl2
-
10 mM, complete inhibition
NAD+
-
weakly competitive
NAD+
-
competitive
NAD+
P26829
FAD-dependent oxidase activity of NADH dehydrogenase is inhibited by NAD+
NEM
-
above 1 mM
NEM
-
0.5 mM, 12% inhibition
nicotinic acid amide
-
slight inhibition
p-hydroxymercuribenzoate
-
-
PCMB
-
0.1 mM, complete inhibition
PCMB
-
complete inhibition at 0.001 mM
PCMB
-
0.005 mM, 50% inhibition
PCMB
-
10 mM, 90% inhibition
phosphate
-
0.033 M, pH 8.5, 70% inhibition
Sodium arsenite
-
10 mM, 44% inhibition
Sodium azide
-
10 mM, 24% inhibition
KCN
-
10 mM, 36% inhibition
additional information
-
no inhibition by rotenone
-
additional information
-
the enzyme is downregulated by NO2-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
additional information
-
activation of the enzyme in erythrocytes by beta-adrenergic agonists
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.03
-
2,6-dichlorophenolindophenol
-
pH 8.0, 50C
0.17
-
benzyl viologen
-
after induction with 1.5% arabinose in culture medium
0.02
-
cytochrome b5
-
-
-
0.0095
-
ferricyanide
-
-
0.049
-
ferricyanide
-
-
0.06
-
ferricyanide
-
after induction with 1.5% arabinose in culture medium
0.44
-
methyl viologen
-
after induction with 1.5% arabinose in culture medium
0.0006
-
NADH
-
-
0.014
-
NADH
-
-
0.0157
-
NADH
-
reaction with 2,6-dichlorophenolindophenol
0.018
-
NADH
-
-
0.0348
-
NADH
-
reaction with ferricyanide
0.0692
-
NADH
-
reaction with 3-(4',5'-dimethylthiazol-2-yl)-diphenyltetrazolium bromide
0.1
-
NADH
-
electron acceptor benzyl viologen, after induction with 1.5% arabinose in culture medium
0.22
-
NADH
-
electron acceptor methyl viologen, after induction with 1.5% arabinose in culture medium
0.31
-
NADH
-
electron acceptor ferricyanide, after induction with 1.5% arabinose in culture medium
0.5
-
NADH
-
pH 8.0, 50C
1.035
-
NADPH
-
reaction with 3-(4',5'-dimethylthiazol-2-yl)-diphenyltetrazolium bromide
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
677
-
ferricyanide
-
-
650
-
NADH
-
electron acceptor methyl viologen, after induction with 1.5% arabinose in culture medium
725
-
NADH
-
electron acceptor benzyl viologen, after induction with 1.5% arabinose in culture medium
1170
-
NADH
-
electron acceptor ferricyanide, after induction with 1.5% arabinose in culture medium
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.08
-
ADP
-
-
0.118
-
NAD+
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
24
-
-
substrate Clostridium acetobutylicum ferredoxin, after induction with 1.5% arabinose in culture medium
392
-
-
substrate methyl viologen, after induction with 1.5% arabinose in culture medium
582
-
-
substrate benzyl viologen, after induction with 1.5% arabinose in culture medium
604
-
-
substrate ferricyanide, after induction with 1.5% arabinose in culture medium
790
-
-
reaction with ferricyanide
additional information
-
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5.2
-
-
NADH-methemoglobin-ferrocyanide reductase activity
6.5
8.5
-
NADH-ferricyanide reductase activity
7.5
8
-
activity with 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
additional information
-
-
-
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-
activity with 3-(4',5'-dimethyl-thiazol-2-yl)2,4-diphenyltetrazolium bromide
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
-
digestion of muscle preparation at 37C with sake-venom phospholipase
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)
Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)
Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
29000
-
-
equilibrium sedimentation
69100
-
-
gel filtration
144000
-
-
gel filtration
480000
-
-
highly aggregated enzyme form, non-denaturing PAGE
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 36000, SDS-PAGE
?
-
x * 17500, SDS-PAGE
?
-
x * 64000, SDS-PAGE
?
-
x * 42000, SDS-PAGE
?
Bacillus subtilis W23
-
x * 64000, SDS-PAGE
-
heterodimer
-
1 * 24000 + 1 * 51000, gel filtration, SDS-PAGE
additional information
-
NdhM, NdhO, and NdhL are NDH subunits specific to photosynthetic/cyanobacterial NDH
additional information
-
NdhM, NdhO, and NdhL are NDH subunits specific to photosynthetic/cyanobacterial NDH. NDH subunits form three types of complexes with different subunit compositions. NDH-1L is required for heterotrophic growth, probably via respiration and CET, while NDH-1M and NDH-1S form the NDH-1MS complex that functions in CO2 concentration
additional information
-
NdhM, NdhO, and NdhL are NDH subunits specific to photosynthetic/cyanobacterial NDH
additional information
Synechocystis sp. PCC6803
-
NdhM, NdhO, and NdhL are NDH subunits specific to photosynthetic/cyanobacterial NDH. NDH subunits form three types of complexes with different subunit compositions. NDH-1L is required for heterotrophic growth, probably via respiration and CET, while NDH-1M and NDH-1S form the NDH-1MS complex that functions in CO2 concentration
-
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
lipoprotein
-
0.0004 mg phospholipid per mg of protein, most of which is cardiolipin with traces of phosphatidylethanolamine and phosphatidylglycerol
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
crystallization with ammonium sulfate
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, stable for several months
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli
-
expression in Escherichia coli
-
genes nuoD, nuoG, nuoM encoding components of the NADH dehydrogenase complex, construction of a signature-tagged mutagenesis library of Pseudomonas aeruginosa, genes regulated by NO2-, anaerobically induced, transcriptional profiling, overview
-
expressed in Escherichia coli, active protein as well as individual subunits are expressed separately
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
K306A
P26829
complete loss of activity
K308A
P26829
one third of oxidase activity of the wild type NADH dehydrogenase
A476S
-
82% of the wild-type NADH dehydrogenase activity
D479A
-
no NADH dehydrogenase activity and NADH oxidase activity
D479K
-
no NADH dehydrogenase activity and NADH oxidase activity
G478A
-
no NADH dehydrogenase activity and NADH oxidase activity which appears to result from
T469A
-
129% of the wild-type NADH dehydrogenase activity