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Information on EC 1.2.1.12 - glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) and Organism(s) Geobacillus stearothermophilus and UniProt Accession P00362
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1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)IUBMB Comments
Also acts very slowly on D-glyceraldehyde and some other aldehydes; thiols can replace phosphate.
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Word Map
- 1.2.1.12
- tetramer
- chloroplast
-
gapcs
- streptococcal
- stearothermophilus
- glomerulonephritis
-
nadp-dependent
-
genorm
-
normfinder
- medicine
- 3-phosphoglycerate
-
phosphofructokinase
- flagellum
-
poststreptococcal
- 1,3-bisphosphoglycerate
-
bestkeeper
- lobster
- glycosomal
-
2.7.1.11
-
glyceraldehyde-phosphate
-
nephritogenic
-
4.1.2.13
- plr
-
2.7.2.3
-
endocapillary
- drug development
- agriculture
- biofuel production
- analysis
- synthesis
- biotechnology
- pharmacology
The taxonomic range for the selected organisms is: Geobacillus stearothermophilus
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
Synonyms
gapdhs, d-glyceraldehyde-3-phosphate dehydrogenase, gadph, gapds, glyceraldehyde-3-phosphate dehydrogenases, plasmin receptor, gapc1, plasminogen-binding protein, gapcp, glyceraldehyde-3 phosphate dehydrogenase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3-phosphoglyceraldehyde dehydrogenase
-
-
-
-
BARS-38
-
-
-
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CP 17/CP 18
-
-
-
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dehydrogenase, glyceraldehyde phosphate
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-
-
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dihydrogenase, glyceraldehyde phosphate
-
-
-
-
G3PD
-
-
-
-
GAPDH
GAPDH1
-
-
-
-
GAPDH2
-
-
-
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glyceraldehyde phosphate dehydrogenase (NAD)
-
-
-
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glyceraldehyde-3-P-dehydrogenase
-
-
-
-
glyceraldehyde-3-phosphate dehydrogenase (NAD)
-
-
-
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GPD
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-
-
-
Gra3PDH
-
-
-
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GraP-DH
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-
-
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Larval antigen OVB95
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-
-
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Major larval surface antigen
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-
-
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NAD+-G-3-P dehydrogenase
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-
-
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NAD-dependent glyceraldehyde phosphate dehydrogenase
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-
-
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NAD-dependent glyceraldehyde-3-phosphate dehydrogenase
-
-
-
-
NAD-G3PDH
-
-
-
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NADH-glyceraldehyde phosphate dehydrogenase
-
-
-
-
P-37
-
-
-
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phosphoglyceraldehyde dehydrogenase
-
-
-
-
Plasmin receptor
-
-
-
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Plasminogen-binding protein
-
-
-
-
TLAb
-
-
-
-
triose phosphate dehydrogenase
-
-
-
-
GAPDH
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
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oxidation
-
-
-
-
reduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
-
-, -, -, -, -, -, -, -, -, -, -, -, -
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
9001-50-7
-
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
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
?
3-phospho-D-glyceroyl phosphate + NADH
D-glyceraldehyde 3-phosphate + phosphate + NAD+
-
-
-
-
r
D-glyceraldehyde 3-phosphate + arsenate + NAD+
3-phospho-D-glyceroyl arsenate + NADH
-
-
-
-
ir
D-glyceraldehyde 3-phosphate + N6-(2-carboxyethyl)-NAD+ + phosphate
3-phospho-D-glyceroyl phosphate + N6-(2-carboxyethyl)-NADH
-
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH + H+
-
activity assay
-
-
?
D-glyceraldehyde 3-phosphate + poly(ethylene glycol)-bound NAD+ + phosphate
3-phospho-D-glyceroyl phosphate + poly(ethylene glycol)-bound NADH
-
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
-
?
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
r
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
r
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH
-
-
-
r
additional information
?
-
-
mutant enzyme C149selenocysteine shows selenoperoxidase activity with tert-butyl hydroperoxide and 3-carboxy 4-nitrobenzenethiol. Wild-type enzyme has no peroxidase activity
-
-
?
additional information
?
-
-
mutant enzyme L187A/P188S is catalytically active not only with NAD+, as the wild-type enzyme, but also with NADP+
-
-
?
NATURAL SUBSTRATE
NATURAL 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
D-glyceraldehyde 3-phosphate + phosphate + NAD+
3-phospho-D-glyceroyl phosphate + NADH + H+
-
activity assay
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NAD+
dimers generated from the tetrameric enzyme are inactive but exhibit cooperativity in NAD+ binding
NAD+
-
poly(ethylene glycol)-bound NAD+ can replace NAD+ as cofactor
NAD+
-
enzyme contains 4 equivalents of firmly bound NAD+
NAD+
-
effects of NAD+ binding on the luminescence of Trp84 and Trp310. NAD+-induced conformational change is sequential and subtle rearrangement in the structure of unligated subunits might be responsible for the negative cooperative behavior of NAD+ binding
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
the produced type I antibody induces a time-dependent decrease in the activity by 80-90% of the active holoenzyme and 25% of the apoenzyme
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1
D-glyceraldehyde 3-phosphate
mutant enzyme D186G and mutant enzyme S48G
0.06
NAD+
-
pH 8.0, 25°C, tetrameric enzyme form, mutant Y283V
0.29
NAD+
-
pH 8.0, 25°C, tetrameric enzyme form, mutant T34Q/T39S/L43Q
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.1
NAD+
-
pH 8.0, 25°C, tetrameric enzyme form, mutant T34Q/T39S/L43Q
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the enzyme possesses precise 222 symmetry. Pairs of active sites are linked through a flexible polypeptide loop which probably mediates the structural changes giving rise to cooperative effects. Three additional salt bridges made by each subunit to others would make a major contribution to thermostability of the tetramer
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
additional information
additional information
dimers generated from the tetrameric enzyme are inactive but exhibit cooperativity in NAD+ binding
additional information
-
dimers generated from the tetrameric enzyme are inactive but exhibit cooperativity in NAD+ binding
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor-diffusion method, enzyme in complex with NAD+ and D-glyceraldehyde 3-phosphate. C149A GAPDH and C149S GAPDH ternary complexes are obtained by soaking the crystals of the corresponding binary complexes (enzyme -NAD+) in a solution containing D-glyceraldehyde 3-phosphate
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C149A
mutant enzyme displays no significant dehydrogenase activity
C149S
low but significant phosphorylating dehydrogenase activity
D186G
behavior in NAD+ binding is similar to that of the wild type enzyme
D186G/E276G
positive cooperativity in binding the coenzyme NAD+
E276G
behavior in NAD+ binding is similar to that of the wild type enzyme
Y46G
behavior in NAD+ binding is similar to that of the wild type enzyme
Y46G/S48G
positive cooperativity in binding the coenzyme NAD+
C149selenocysteine
-
mutant enzyme has selenoperoxidase activity
D282G
-
enzyme exists as dimer and tetramer, the tetramer is inactive, the dimer is slightly active, 650fold decrease in turnover number for NAD+, 5.8fold increase in Km-value for NAD+ compared to wild-type enzyme
L187A/P188S
-
the mutant is catalytically active not only with NAD+, as the wild-type enzyme, but also with NADP+
N313T
-
mutant enzyme with a drastic decrease in thermostability, weakening of cooperative interactions between the catalytic and the cofactor domains and an inefficient binding of NAD+, mutant enzyme exists only as tetramer, 65fold decrease in turnover number for NAD+, 50fold increase in Km-value for NAD+ compared to wild-type enzyme
T34Q/T39S/L43Q
-
drastic decrease in thermostability, inefficient NAD+ binding, enzyme exists as dimer and tetramer, the tetramer is inactive, the dimer is slightly active, 650fold decrease in turnover number for NAD+, 4fold increase in Km-value for NAD+ compared to wild-type enzyme
W310F
-
mutant enzyme with a drastic decrease in thermostability, mutant enzyme exists only as tetramer, 2fold increase of Km-value for NAD+, 1.3fold decrease in turnover number compared to wild-type enzyme
W84F
-
slightly lower Km-values for NAD+ and glyceraldehyde 3-phosphate, slightly higher Km-value for phosphate. The construction of the mutant permitts the identification of the individual fluorescence and phosphorescence characteristics of the two Trp residues W84 and W310 in the native enzyme
Y283V
-
mutant enzyme with a drastic decrease in thermostability, dimeric form is inactive, KM-value and turnover-number of tetramer are nearly identical to that of the wild-type
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60 - 70
-
retains structural integrity and enzymatic activity up to
62
-
maximum of thermal transition peak of tetrameric form of mutant apoenzyme N313T
64.8
65.4
-
maximum of thermal transition peak of dimeric mutant apoenzyme Y46G/S48G
65.5
-
maximum of thermal transition peak of dimeric mutant apoenzyme Y46G/R52G
68.4
-
maximum of thermal transition peak of tetrameric mutant apoenzyme Y283V
70.3
-
maximum of thermal transition peak of tetrameric mutant apoenzyme D283G
70.7
-
maximum of thermal transition peak of tetrameric mutant apoenzyme W310F
71
-
maximum of thermal transition peak of dimeric mutant apoenzyme D282G
73.5
-
maximum of thermal transition peak of dimeric mutant apoenzyme Y283V
78.5
-
maximum of thermal transition peak of tetrameric form of wild-type apoenzyme
additional information
-
three salt bridges made by each subunit to others would make a major contribution to thermostability of the tetramer
64.8
-
maximum of thermal transition peak of dimeric mutant apoenzyme T34Q/T39S/L43Q
64.8
-
maximum of thermal transition peak of tetrameric mutant apoenzyme T34Q/T39S/L43Q
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
5.0 M guanidine-HCl, rapid and irreversible inactivation at 30°C
-
8.0 M urea, unusually resistant at 30°C, 40°C and 50°C. Rapid inactivation at 55°C and at 60°C
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, in 67% saturated ammonium sulfate solution containing EDTA and dithiothreitol, stable for months
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
using gel filtration on a AcA-34 column, and a Q-Sepharose and phenyl-Sepharose column
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cloned into the pBluescript vector for expression in Escherichia coli GM-109 cells
-
expression of wild-type and mutant enzyme W84F in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lambeir, A.M.; Loiseau, A.M.; Kuntz, D.A.; Vellieux, F.M.; Michels, P.A.M.; Opperdoes, F.R.
The cytosolic and glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei. Kinetic properties and comparison with homologous enzymes
Eur. J. Biochem.
198
429-435
1991
Geobacillus stearothermophilus, Oryctolagus cuniculus, Homo sapiens, Trypanosoma brucei
Corbier, C.; Clermont, S.; Billard, P.; Skarzynski, T.; Branlant, C.; Wonacott, A.; Branlant, G.
Probing the coenzyme specificity of glyceraldehyde-3-phosphate dehydrogenases by site-directed mutagenesis
Biochemistry
29
7101-7106
1990
Geobacillus stearothermophilus
Skarzynski, T.; Moody, P.C.E.; Wonacott, A.J.
Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 A resolution
J. Mol. Biol.
193
171-187
1987
Geobacillus stearothermophilus
Katayama, N.; Hayakawa, K.; Urabe, I.; Okada, H.
Kinetic properties of N6-(2-carboxyethyl)-NAD(H) and poly(ethylene glycol)-bound NAD(H) for alcohol, lactate, malate and glyceraldehyde-3-phosphate dehydrogenase from different organisms
Enzyme Microb. Technol.
6
538-542
1984
Geobacillus stearothermophilus, Oryctolagus cuniculus, Thermus thermophilus
-
Harris, J.I.; Hocking, J.D.; Runswick, M.J.; Suzuki, K.; Walker, J.E.
D-glyceraldehyde-3-phosphate dehydrogenase. The purification and characterisation of the enzyme from the thermophiles Bacillus stearothermophilus and Thermus aquaticus
Eur. J. Biochem.
108
535-547
1980
Geobacillus stearothermophilus, Oryctolagus cuniculus, Thermus aquaticus
Gabellieri, E.; Rahuel-Clermont, S.; Branlant, G.; Strambini, G.B.
Effects of NAD+ binding on the luminescence of tryptophans 84 and 310 of glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus
Biochemistry
35
12549-12559
1996
Geobacillus stearothermophilus
Biesecker, G.; Harris, J.I.; Thierry, J.C.; Walker, J.E.; Wonacott, A.J.
Sequence and structure of D-glyceraldehyde 3-phosphate dehydrogenase from Bacillus stearothermophilus
Nature
266
328-333
1977
Geobacillus stearothermophilus
Harris, J.I.; Waters, M.
Glyceraldehyde-3-phosphate dehydrogenase
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
13
1-49
1976
Geobacillus stearothermophilus, Bacillus cereus, Bos taurus, Saccharomyces cerevisiae, Canis lupus familiaris, Gallus gallus, Oryctolagus cuniculus, Escherichia coli, Felis catus, Hippoglossus sp., Homo sapiens, Lobster, Meleagris gallopavo, Pisum sativum, Rattus norvegicus, Acipenser sp., Sus scrofa, Thermus aquaticus
-
Amelunxen, R.E.
Glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus
Methods Enzymol.
41
268-273
1975
Geobacillus stearothermophilus
Boschi-Muller, S.; Muller, S.; Van Dorsselaer, A.; Bock, A.; Branlant, G.
Substituting selenocysteine for active site cysteine 149 of phosphorylating glyceraldehyde 3-phosphate dehydrogenase reveals a peroxidase activity
FEBS Lett.
439
241-245
1998
Geobacillus stearothermophilus
Roitel, O.; Sergienko, E.; Branlant, G.
Dimers generated from tetrameric phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus are inactive but exhibit cooperativity in NAD binding
Biochemistry
38
16084-16091
1999
Geobacillus stearothermophilus (P00362), Geobacillus stearothermophilus
Roitel, O.; Ivinova, O.; Muronetz, V.; Nagradova, N.; Branlant, G.
Thermal unfolding used as a probe to characterize the intra- and intersubunit stabilizing interactions in phosphorylating D-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus
Biochemistry
41
7556-7564
2002
Geobacillus stearothermophilus
Didierjean, C.; Corbier, C.; Fatih, M.; Favier, F.; Boschi-Muller, S.; Branlant, G.; Aubry, A.
Crystal structure of two ternary complexes of phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus with NAD and D-glyceraldehyde 3-phosphate
J. Biol. Chem.
278
12968-12976
2003
Geobacillus stearothermophilus (P00362)
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