Information on EC 1.2.1.12 - glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) and Organism(s) Homo sapiens and UniProt Accession P04406

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Homo sapiens
UNIPROT: P04406
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea


The taxonomic range for the selected organisms is: Homo sapiens

EC NUMBER
COMMENTARY hide
1.2.1.12
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RECOMMENDED NAME
GeneOntology No.
glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+
show the reaction diagram
ordered ter bi mechanism characterized by the sequential addition of NAD+, glyceraldehyde 3-phosphate and phosphate to the enzyme and the sequential release of 3-phospho-D-glyceroyl phosphate and NADH from the enzyme
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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reduction
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oxidation
redox reaction
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-
-
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reduction
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Bifidobacterium shunt
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Biosynthesis of antibiotics
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Biosynthesis of secondary metabolites
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Carbon fixation in photosynthetic organisms
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formaldehyde assimilation III (dihydroxyacetone cycle)
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gluconeogenesis I
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gluconeogenesis III
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glycerol degradation to butanol
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Glycolysis / Gluconeogenesis
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glycolysis I (from glucose 6-phosphate)
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glycolysis II (from fructose 6-phosphate)
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glycolysis III (from glucose)
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glycolysis IV (plant cytosol)
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heterolactic fermentation
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Metabolic pathways
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Microbial metabolism in diverse environments
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sucrose biosynthesis I (from photosynthesis)
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superpathway of glucose and xylose degradation
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glycolysis
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SYSTEMATIC NAME
IUBMB Comments
D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating)
Also acts very slowly on D-glyceraldehyde and some other aldehydes; thiols can replace phosphate.
CAS REGISTRY NUMBER
COMMENTARY hide
9001-50-7
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH + H+
show the reaction diagram
3-phospho-D-glyceroyl phosphate + NADH
D-glyceraldehyde 3-phosphate + phosphate + NAD+
show the reaction diagram
acetaldehyde + phosphate + NAD+
acetyl phosphate + NADH
show the reaction diagram
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enzyme form E6.6 shows 27% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E6.8 shows 9% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E8.5 shows 6% of the actity with D-glyceraldehyde 3-phosphate, enzyme form E9.0 shows 0.4% of the activity with D-glyceraldehyde 3-phosphate
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-
?
arsenate + GSH + NAD+ + glyceraldehyde 3-phosphate
arsenite + ?
show the reaction diagram
-
-
-
-
?
butyraldehyde + phosphate + NAD+
butyryl phosphate + NADH
show the reaction diagram
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enzyme form E6.6 shows 10% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E6.8 shows 15% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E8.5 shows 12% of the actity with D-glyceraldehyde 3-phosphate, enzyme form E9.0 shows 0.9% of the activity with D-glyceraldehyde 3-phosphate
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-
?
D-glyceraldehyde 3-phosphate + arsenate + NAD+
3-phospho-D-glyceroyl arsenate + NADH
show the reaction diagram
-
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
show the reaction diagram
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH + H+
show the reaction diagram
DL-glyceraldehyde + phosphate + NAD+
D-glyceroyl phosphate + NADH
show the reaction diagram
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enzyme form E6.6 shows no activity, enzyme form E6.8 shows 2.5% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E8.5 shows 30% of the actity with D-glyceraldehyde 3-phosphate, enzyme form E9.0 shows 3.0% of the activity with D-glyceraldehyde 3-phosphate
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-
?
erythrose 4-phosphate + phosphate + NAD+
? + NADH
show the reaction diagram
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enzyme form E6.6 shows no activity, enzyme form E6.8 shows 1.2% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E8.5 shows 25% of the actity with D-glyceraldehyde 3-phosphate, enzyme form E9.0 shows 1.5% of the activity with D-glyceraldehyde 3-phosphate
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-
?
glucose + phosphate + NAD+
? + NADH
show the reaction diagram
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enzyme form E6.6 shows no activity, enzyme form E6.8 shows 0.6% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E8.5 shows 6.0% of the actity with D-glyceraldehyde 3-phosphate, enzyme form E9.0 shows 0.8% of the activity with D-glyceraldehyde 3-phosphate
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-
?
propionaldehyde + phosphate + NAD+
propionyl phosphate + NADH
show the reaction diagram
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enzyme form E6.6 shows 33% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E6.8 shows 12% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E8.5 shows 10% of the actity with D-glyceraldehyde 3-phosphate, enzyme form E9.0 shows 0.8% of the activity with D-glyceraldehyde 3-phosphate
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-
?
valeraldehyde + phosphate + NAD+
pentanoyl phosphate + NADH
show the reaction diagram
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enzyme form E6.6 shows no activity, enzyme form E6.8 shows 19% of the activity with D-glyceraldehyde 3-phosphate, enzyme form E8.5 shows 18% of the actity with D-glyceraldehyde 3-phosphate, enzyme form E9.0 shows 0.9% of the activity with D-glyceraldehyde 3-phosphate
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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
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH + H+
show the reaction diagram
P04406
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-
-
r
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
show the reaction diagram
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH + H+
show the reaction diagram
-
-
-
-
?
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADH
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each subunit is bound to one NAD+
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn
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enzyme form E8.5 contains 0.64 gatoms of zinc per mol of enzyme, enzyme form E9.0 contain 2.76 gatom of zinc per mol of enzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-hydroxy-2-oxo-3,3-bis(2-aminoethyl)-1-triazene
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H2O2
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2,3-diphosphoglycerate
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acetylleucine chloromethyl ketone
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binds to GAPDH to modulate the conformation of the enzyme, the modified enzyme is susceptible to chymotrypsin-like protease activity, cleavage at TRp195-Arg196; irreversible inhibition, enzyme modified by acetylleucine chloromethyl ketone is deduced to be digested at the peptide bond Trp196-Arg196
ADP
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moderately inhibits arsenate reductase activity
CGP-3466
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deprenyl-related compound that inhibits the pro-apoptotic activity of GAPDH
D-glyceraldehyde 3-phosphate
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substrate inhibition
demethylasterriquinone B1
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binding of demethylasterriquinone B1 toGAPDH could disrupt phosphatase acting upon phosphatidylinositol lipids and thereby potentiate insulin signaling via the phosphatidylinositol-3-kinase pathway
diepoxybutane
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incubation of GAPDH with bis-electrophiles results in inhibition of its catalytic activity, but only at high concentrations of diepoxybutane
ferriprotoporphyrin IX
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enzyme is partially inactivated through oxidation of critical thiols
FK506-binding protein 36
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i.e. FKBP36. The interaction between FKBP36 and GAPDH directly inhibits the catalytic activity of GAPDH. FKBP36 expression causes a significant reduction of the GAPDH level and activity in COS-7 cells. GAPDH is depleted by FKBP36 expression, particularly in the cytosolic fraction
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iodoacetamide
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iodoacetate
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Koningic acid
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inhibits arsenate reductase activity and activity with D-glyceraldehyde 3-phosphate, phosphate and NAD+
N-acetylcysteine
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5 mM N-acetylcysteine significantly reduces G3PD activation induced by both H2O2 and ferric protoporphyrin IX
NAD+
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competitive against NADH
NO3-
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uncompetitive inhibitor with NAD+, dead end inhibitor
additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
doxorubicin
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treatment results in increased nuclear localization of expressed wild-type GAPDH, where it protects telomeres against rapid degradation, concomitant with increased resistance to the growth-inhibitory effects of the drug
Ferric protoporphyrin IX
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145% increase of activity at 0.04 mM ferric protoporphyrin IX after 30 min exposure to stauroporin
gemcitabine
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treatment results in increased nuclear localization of expressed wild-type GAPDH, where it protects telomeres against rapid degradation, concomitant with increased resistance to the growth-inhibitory effects of the drug
Triton X-100
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additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.01 - 0.018
1,3-diphosphoglyceric acid
0.002 - 0.172
3-phospho-D-glyceroyl phosphate
0.00025 - 3.7
D-glyceraldehyde 3-phosphate
0.1
DL-glyceraldehyde
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enzyme form E8.5, pH 7
0.119 - 0.127
erythrose 4-phosphate
0.01 - 100
NAD+
0.01
NADH
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4 - 9.9
phosphate
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
199 - 234
D-glyceraldehyde 3-phosphate
199 - 234
NAD+
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.1
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pH 8.5, 25C
8.6
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enzyme form E6.6
13
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enzyme form E6.8
68.1
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enzyme from liver
158
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enzyme form E8.5
620
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enzyme form E9.0
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 8.3
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7
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enzyme form E6.8, two pH optima: pH 7.0 and pH 8.5, with activity between pH 7.5 and pH 8.0 being rather low
7.2 - 7.3
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reaction with 3-phospho-D-glyceroylphosphate
7.3 - 8.8
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enzyme isolated from sarcoma tissue, broad
8 - 8.3
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reaction with D-glyceraldehyde 3-phosphate
8 - 9
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8.6
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enzyme isolated from normal tissue, sharp optimum
9.8
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enzyme form E8.5, D-glyceraldehyde 3-phosphate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.8
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above, sharp decline in activity for enzyme of patients with chronic myeloid leukemia, no similar sharp decline for enzyme of healthy subjects
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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human juvenile costal chondrocyte cell
Manually annotated by BRENDA team
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lung, microvascular
Manually annotated by BRENDA team
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in both fetal and senior cells, considerable GAPDH is present in intracellular domains characterized by significantly reduced catalysis. Human cells contain significant intracellular levels of enzymatically inactive GAPDH which is age-independent
Manually annotated by BRENDA team
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KB cell line ATCC CCL17
Manually annotated by BRENDA team
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normal human ovarian surface epithelial cell line
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
protein complex containing GAPDH and androgen receptor in the cytosol
Manually annotated by BRENDA team
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protein complex containing GAPDH and androgen receptor in the nucleus
Manually annotated by BRENDA team
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enzyme form E6.8, E8.5 and E9.0
Manually annotated by BRENDA team
additional information
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the subcellular localization of enzyme form E6.6 is uncertain
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Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
36000
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SDS-PAGE, native enzyme
29500
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4 * 29500, enzyme form E8.5, SDS-PAGE
33000
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4 * 33000, enzyme form E9.5, SDS-PAGE
37000
-
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37672
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4 * 37672, MALDI-TOF mass spectrometry
61000
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1 * 58000 + 1 * 61000, enzyme form E6.6, SDS-PAGE
98000
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enzyme form E6.6, gel filtration
120000
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enzyme form E8.5, gel filtration
133000
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enzyme form E9.0, gel filtration
142000
144000
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gel filtration
150000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
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monomer
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1 * 36000, SDS-PAGE
dimer
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1 * 58000 + 1 * 61000, enzyme form E6.6, SDS-PAGE
homotetramer
tetramer
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphorylation
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side-chain modification
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dimethylation, deamidation, and methionine oxidation
additional information
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4-hydroxy-2-nonenal-modified GAPDH is degraded by cathepsin G
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
the structure is presented at 2.5 A resolution
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a high-resolution structure of 1.75 A is reported
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crystallization of a a highly soluble form of GAPDS truncated at the N-terminus, amino acids 69398. The structure in complex with NAD+ and phosphate maps the two anion-recognition sites within the catalytic pocket that correspond to the conserved Ps site and Pi site identified in other organisms. The structure in complex with NAD+ and glycerol shows serendipitous binding of glycerol at the Ps and Pi sites; in complex with NAD+ and phosphate, hanging drop vapor diffusion method, using 20% (w/v) poly(ethylene glycol) 3350, 0.2 M sodium/potassium phosphate and 10% (v/v) ethylene glycol or in complex with NAD+ and glycerol, hanging drop vapor diffusion method, 20% PEG 3350, 0.2 M Na2SO4, 10% (v/v) ethylene glycol and 0.1 M Bis-Tris propane (pH 6.5)
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
acetylleucine chloromethyl ketone binds to GAPDH to modulate the conformation of the enzyme, the modified enzyme is susceptible to chymotrypsin-like protease activity, cleavage at TRp195-Arg196
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binding to erythrocyte membranes stabilizes the enzyme at 4C
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
at -20C storage after dialysis following the first (NH4)2SO4 fractionation step during purification, normal muscle and leukocyte enzyme is stable. Enzyme from chronic myeloid leukemia patients and sarcoma tissue loses about 80% of activity.
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
analytical centrifugation
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by affinity chromatography on a Hi-Trap chelating column charged with nickel sulfate, the His tag is cleaved and the enzyme is purified by an additional gel filtration step
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Ni-NTA agarose resin chromatography and Hi-Load 16/60 Superdex gel filtration
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4 enzyme forms: E6.6, E6.8, E8.5 and E9.0
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DEAE-Sepharose column chromatography, ammonium sulfate precipitation, phenyl-Sepharose 6 column chromatography, and Superose 6 gel filtration
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from normal leukocytes of healthy subjects, leukocytes of chronic myeloid leukemia patients and from sarcoma tissue
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GST-fusion proteins are expressed in Escherichia coli and subsequently purified by absorption to glutathione-Sepharose beads, GST is seperated by digestion with thrombin protease
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Ni-Sepharose column chromatography and Superdex S75 gel filtration
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Ni2+-NTA agarose resin chromatography
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phenyl Sepharose column chromatography
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red blood cell cytosol is prepared by hypotonic shock or freeze-thawing cycles, membranes are prepared by hypotonic lysis
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use of immunoaffinity column chromatography
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using Ni-NTA resin and a HiTrap Blue column, the His tag is removed
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli strainW3CG and in HeLa cells
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expressed in prostate cancer cell lines PC-3 and LNCaP
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subcloned into the pET15b vector for expression in Escherichia coli cells
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expressed in Escherichia coli BL21(DE3)-R3 cells; expression in Escherichia coli
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expressed in Escherichia coli TRG8 cells
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expressed in Escherichia coli; expression in COS-7 cells
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expressed in HEK-293T cells
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expressed in MCF-7 cells
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expression in 293Tcells and HepG2.2.15 cells
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expression in COS-7 cell
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expression in Escherichia coli
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into a pGEX-5X-3 and a pGFP-C2 vector
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subcloned into a pET14b vector for expression in Escherichia coli BL21DE3 cells
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
24 h after irradiation at 5 gray, nuclear GAPDH levels increase 2.6fold, whereas total GAPDH increases only 1.2fold. Knockdown of GAPDH by siRNA leads to sensitization to X-ray-induced cell death
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GAPDH-small interfering RNA knockdown sensitizes the cells to methyl methane sulfonate and bleomycin, which generate lesions that are repaired by APE1, but cells show normal sensitivity to 254-nm UV. GAPDH knockdown cells exhibit an increased level of spontaneous abasic sites in the genomic DNA as a result of diminished APE1 endonuclease activity
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C149A
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mutant has almost completely lost the ability to bind telomere. Upon expression in A-549 cells, mutant localizes to the nucleus but is unable to confer any significant protection of telomeres against chemotherapy-induced degradation or growth inhibition
C152G
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mutant retains the ability to interact with but is unable to reactivate DNA repair enzyme APE1
C156G
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mutant retains the ability to interact with but is unable to reactivate DNA repair enzyme APE1
D32A
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mutant is unable to bind NAD+, is enzymatically inactive and has almost completely lost the ability to bind telomere. Upon expression in A-549 cells, mutant localizes to the nucleus but is unable to confer any significant protection of telomeres against chemotherapy-induced degradation or growth inhibition
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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functions are of chemotherapeutic interest, structure is a necessity for structure-based drug design
medicine