Any feedback?
Please rate this page
(all_enzymes.php)
(0/150)

BRENDA support

1.2.1.12: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

This is an abbreviated version!
For detailed information about glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), go to the full flat file.

Word Map on EC 1.2.1.12

Reaction

D-glyceraldehyde 3-phosphate
+
phosphate
 +
NAD+
=
3-phospho-D-glyceroyl phosphate
 +
NADH
 +
H+

Synonyms

3-phosphoglyceraldehyde dehydrogenase, A4-GAPDH, A4-glyceraldehyde-3-phosphate dehydrogenase, AB-GAPDH, AnBn-GAPDH, AsGAPDH, At3g04120, BARS-38, CbbG, CgGAP, Clo1313_2095, complement-C3-binding protein, CP 17/CP 18, Ctherm_Gapdh, cytosolic NAD-dependent glyceraldehyde 3-P dehydrogenase, cytosolic phosphorylating glyceraldehyde-3-phosphate dehydrogenase, D-glyceraldehyde-3-phosphate dehydrogenase, D-glyceraldehyde-3-phosphate: NAD+ oxidoreductase (phosphorylating), dehydrogenase, glyceraldehyde phosphate, dihydrogenase, glyceraldehyde phosphate, EcGAPDH, EcGAPDH1, FgGAPDH, FhGAPDH, G3PD, G3PDH, Ga3P dehydrogenase, Ga3PDHase, GADPH, GAP, GAP1, gap2, GapA, GapB, GAPC, GapC-1, GapC1, GapC2, GAPCp, GAPCp1, GAPCp2, GAPD, GAPDH, GAPDH type 1, GAPDH1, GAPDH2, GAPDH3, GAPDHS, GAPDS, GAPN, GBS GAPDH, glyceraldehyde 3-phosphate dehydrogenase, glyceraldehyde 3-phosphate dehydrogenase-S, glyceraldehyde phosphate dehydrogenase (NAD), glyceraldehyde-3 phosphate dehydrogenase, glyceraldehyde-3-P-dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase (NAD), glyceraldehyde-3-phosphate dehydrogenase 1, glyceraldehyde-3-phosphate dehydrogenase, type I, glyceraldehyde-3-phosphate dehydrogenase-spermatogenic protein, glyceraldehyde-3-phosphate dehydrogenase-spermatogenic protein GAPDHS, glyceraldehyde-3-phosphate dehydrogenases, GPD, GPD2, Gra3PDH, GraP-DH, H.c-C3BP, hGAPDH, HsGAPDH, kmGAPDH1p, Larval antigen OVB95, Major larval surface antigen, Mtb-GAPDH, NAD+-dependent GAPDH, NAD+-dependent glyceraldehyde 3-phosphate dehydrogenase, NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase, NAD+-G-3-P dehydrogenase, NAD+-GAPDH, NAD-dependent Ga3PDHase, NAD-dependent glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent glyceraldehyde phosphate dehydrogenase, NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, NAD-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, NAD-dependent phosphorylating glyceraldehyde-3-phosphate dehydrogenase, NAD-G3PDH, NAD-GAPDH, NADH-glyceraldehyde phosphate dehydrogenase, P-37, p-GAPDH, PfGAPDH, phosphoglyceraldehyde dehydrogenase, phosphorylating NAD+-dependent GAPDH, Plasmin receptor, Plasminogen-binding protein, plastidial glyceraldehyde-3-phosphate dehydrogenase, pmGAPDH, PyGapdh, rmGAPDH, Rv1436, somatic GAPD, somatic glyceraldehyde 3-phosphate dehydrogenase, sperm-specific GAPDS, sperm-specific glyceraldehyde 3-phosphate dehydrogenase, sperm-specific glyceraldehyde-3-phosphate dehydrogenase, TaeNAD-GAPDH, TagapC, TDH1, TDH2, TDH3, TLAb, triose phosphate dehydrogenase, UDG, uracil-DNA glycosylase, vGPD

ECTree

     1 Oxidoreductases
         1.2 Acting on the aldehyde or oxo group of donors
             1.2.1 With NAD+ or NADP+ as acceptor
                1.2.1.12 glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

Crystallization

Crystallization on EC 1.2.1.12 - glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
X-ray diffraction structure determination and analysis at 2.4 A resolution, structure modeling
resolution to 2.2 A. space group I222
-
crystalline enzyme does not contain NAD+
-
purified native tetrameric enzyme with either three or four bound NAD+ molecules, bGAPDH can be crystallized directly from isotonic extracts of ROS, X-ray diffraction structure determination and analysis at 1.93 A and 1.54 A resolution, respectively, molecular replacement using the coordinates of one monomer of rabbit-muscle GAPDH, PDB ID 1J0X, without ligand and water to search the initial model, modelling
GAPDH in the apo and holo (enzyme in complex with NAD+) state, hanging drop vapor diffusion method, using 16-20% (w/v) PEG 3000 and 0.2 M NaCl in 0.1 M HEPES, pH 7.5
structure in absence and presence of NAD+ and structure of the ternary enzyme-cofoactor-substrate complex to 2.0 A resolution. The active site can accomodate the substrate in multiple conformations at multiple locations during the initial encounter. the C-3 phosphate group clearly prefers the so-called new phosphate site for initial binding
GADPH in complex wit NAD+, computational modelling
-
after addition of NAD+ to the apoprotein
-
native, non-modified and selenium-modified enzymes, 5.5 mg/ml protein in 10 mM HEPES, pH 7.5, and 1.43 M sodium citrate, 18°C, 3 days, method optimization, crystals from the selenium modified enzyme are soaked for 10 min in 5 mM NAD+ dissolved in mother liquor with or without 25% trehalose, X-ray diffraction structure determination and analysis at 1.64-2.14 A resolution using single-wavelength anomalous dispersion (SAD) phasing with a selenium-modified enzyme, molecular replacement
purified recombinant enzyme GAPDH complexed with trehalose, hanging drop vapour diffusion method, mixing of 20 mg/ml protein in 20 mM Tris, 130 mM NaCl pH 7.5, with reservoir solution containing 2.8 M ammonium sulfate, 0.1 M MES, pH 5.5-6.5, 4°C, two to three weeks, GAPDH crystals are treated with a cryoprotectant consisting of 15% v/v trehalose at -173°C, X-ray diffraction structure determination and analysis at 2.1 A resolution, molecular replacement using the Escherichia coli GAPDH structure (PDB ID 1s7c) as a starting model
purified recombinant isozyme EcGAPDH1, sitting drop vapour diffusion method, mixing of 240 nl of 30 mg/ml protein in 4 mM NaCl, and 5 mM Tris-HCl pH 8.0, with 240 nl of reservoir solution containing reservoir solution consisting of 100 mM sodium acetate, pH 4.6, 30% w/v PEG 400,and 200 mM calcium acetate, and equilibration against 0.1 ml of reservoir solution, 1 week, method optimization, X-ray diffraction structure determination and analysis at 1.88 A resolution, molecular replacement using the structure of GAPDH from methicillin-resistant Staphylococcus aureus MRSA252 (PDB ID 3lvf) as search model, model building
structure determination by formation of soluble recombinant rat sperm glyceraldehyde-3-phosphate dehydrogenase as a heterotetramer with the Escherichia coli glyceraldehyde-3-phosphate dehydrogenase in a ratio of 1:3. Glyceraldehyde 3-phosphate binds in the Ps pocket in the active site of the sperm enzyme subunit in the presence of NAD
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
holoenzyme and apoenzyme
-
structure at 1.8 A resolution
-
a high-resolution structure of 1.75 A is reported
-
analysis of human GAPDH crystal structure, PDB ID 1U8F
crystallization of a a highly soluble form of GAPDS truncated at the N-terminus, amino acids 69–398. 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)
purified recombinant apo-enzyme tGAPDHS, hanging-drop vapor-diffusion method, 10 mg/ml in 10 mM HEPES, pH 7.5, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, and 0.01% of sodium azide, is mixed in a 1:1 volume ratio with reservoir solution containing 0.2 M Na2SO4, 0.1 M Bis-Tris propane, pH 6.5, and 20% PEG 3350, 20°C, 2 days, crystallization of purified recombinant holoenzyme tGAPDHS in complex with NAD+, hanging-drop vapor-diffusion method, 10 mg/ml in 10 mM HEPES, pH 7.5, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, and 0.01% of sodium azide, is mixed in a 1:1 volume ratio with reservoir solution 0.2M NaNO3, and 20% PEG3350, 20°C, 2 days, X-ray diffraction structure determination and analysis at a.86 A (apoenzyme) and 1.73 A (holoenzyme) resolutions, method screening
the structure is presented at 2.5 A resolution
diffraction data to 2.3 A resolution are collected
-
purified recombinant apo-enzyme tGAPDHS, hanging-drop vapor-diffusion method, 3 mg/ml protein in PBS is mixed in a 1:1 volume ratio with reservoir solution containing 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane, pH 6.5, and 20% PEG 3350, 20°C, 6 days, X-ray diffraction structure determination and analysis at 2.01 A resolution
purified recombinant N-terminally His-tagged enzyme, hanging drop vapor diffusion method, mixing of 10 mg/ml protein with reservoir solution containing either 12.9% w/v PEG 2000, 50 mM acetate buffer, pH 5.2, and 6.4% w/v PEG 200, or 2.5% w/v PEG 1000, 50 mM acetate buffer, pH 4.8, and 25.7% w/v PEG 2000 MME, 18°C, 3 days, X-ray diffraction structure determination and analysis at 2.40 A and 1.94 A resolutions, respectively
-
sitting-drop vapour-diffusion method, crystallized in space group P2(1)2(1)2(1) with a tetramer in the asymmetric unit, crystals solved at 2.4 A
-
in complex with NAD+ and sulfate, using ammonium sulfate (50 mM) and Bis-Tris (50 mM, pH 6.1). Native enzyme, hanging drop vapor diffusion method, using 16% PEG3350 (w/v) and citric acid (0.1 M, pH 4.1)
structures of NAD-free, NAD-bound and sulfate-soaked forms, to 2.3, 1.86 and 3.77 A resolution, respectively. Residue Phe37 forms a bottleneck to improve NAD-binding and also combines with Pro193 and Asp35 as key conserved residues for NAD-specificity. The binding of NAD alters the side-chain conformation of Phe37 with a 90° rotation related to the adenine moiety of NAD, concomitant with clamping the active site about 0.6 A from the open to closed form, producing an increased affinity specific for NAD
enzyme carrying a fluorescent NAD+ derivative at 2.7 A resolution
-
structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues ADPribose and thio-NAD+. The crystals of both GAPDH complexes belong to the same space group C2 as holeenzyme or apoenzyme, but with different unit-cell parameters
crystals of tag-free protein diffracts X-rays to 2.6 A resolution, of the His-tagged protein to 4.0 A
-
the crystal structure is solved at 2.25 A resolution
structure determination by formation of soluble recombinant rat sperm glyceraldehyde-3-phosphate dehydrogenase as a heterotetramer with the Escherichia coli glyceraldehyde-3-phosphate dehydrogenase in a ratio of 1:3. Refinement to 2.2 A for the holo enzyme, to 2.4 A for the complex with glyceraldehyde 3-phosphate. Glyceraldehyde 3-phosphate binds in the Ps pocket in the active site of the sperm enzyme subunit in the presence of NAD
purified apo-form GAPDH3, by vapor-diffusing method, mixing 10 mg/mL protein with a reservoir solution containing 12% (w/v) PEG 3350, 0.1 M sodium malonate, pH 4.0, 2 days, at 14°C, X-ray diffraction structure determination and analysis at 2.49 A resolution, modeling
quaternary structure of the GAPDH A2B2 heterotetramer, PDB ID 2PKQ, from Spinacia oleracea, crystallographic subunits O (GapB) and R (GapA)
hanging drop vapor diffusion method, using 0.1 M Tris-HCl pH 8.2, 28% (w/v) PEG 3350, at 25°C
to 2.0 A resolution. Space group P21
wild type holo and apoenzymes and mutant enzymes C151S, C151G and C151S/H178N in complex with NAD+ and D-glyceraldehyde 3-phosphate, hanging drop vapor diffusion method, the wild-type holoenzyme and apoenzyme are crystallized from 0.1 M Tris-HCl, pH 8.5, and 20% (w/v) PEG 4000 at 4°C and from 0.1 M Tris-HCl, pH 8.2, and 32% (w/v) PEG 3350 at 25°C, respectively. Crystals of active-site mutants in complex with NAD+ (C151S, C151G, and C151S/H178N) grow at 25°C from 0.1 M Tris-HCl, pH 8.5, and 28% (w/v) PEG 4000, from 0.1 M Tris-HCl, pH 8.2, and 30% (w/v) PEG 4000, and from 0.1 M Tris-HCl, pH 8.5, and 30% (w/v) PEG 4000, respectively, while mutant H178N in complex with NAD+ crystallizes from 0.1 M Tris-HCl, pH 8.2, and 30% (w/v) PEG 4000 at 4°C
purified wild-type enzyme in apo-form, in a mixed apo/holo-state (2 subunits with bound NAD and two without), and in a ternary complex, and purified mutant C152S enzyme in ternary complex, hanging drop vapor diffusion method, mixing of 15 mg/ml protein in 25 mM HEPES, pH 7.35, 00 mM NaCl, and 5 mM 2-mercaptoethanol with reservoir solution containing 20-28% PEG 4000, 0.1 M MES, pH 6.5, at 22°C, X-ray diffraction structure determination and analysis at 2.0 A resolution
purified recombinant detagged group B streptococcus GAPDH enzyme, hanging drop vapour diffusion method, mixing of 20 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 100 mM NaCl, with reservoir solution containing 2 M ammonium sulfate, 1 M lithium sulfate, and 0.1 M Tris-HCl pH 8.5, cryoprotection by addition of 5% glycerol, X-ray diffraction structure determination and analysis at 1.36 A resolution, molecular replacement using the published structure of GAPDH as a search model (PDB ID 4qx6)
crystallization of the ternary complex between GAPDH, intrinsically disordered protein CP12 and NAD+ in both the absence and presence of copper. The oxidized CP12 proten becomes partially structured upon GAPDH binding. The C-terminus of CP12 is inserted into the active-site region of GAPDH, resulting in competitive inhibition of GAPDH
in complex with CP12 and NAD+, hanging drop vapor diffusion method, using 20% (w/v) PEG3350 and 0.2 M magnesium acetate
hanging drop vapour diffusion method, enzyme in complex with the covalently bound GAP analogue, 3-(p-nitrophenoxycarboxyl)-3-ethylene propyl dihydroxyphosphonate, at an improved resolution of 2.0-2.5 A
-
molecular dynamics simulations based on PDB entry 1K3T. The first stage of the reaction (oxidoreduction) takes place in the Pi site (energetically more favourable), with the formation of oxyanion thiohemiacetal and thioacylenzyme intermediates without acid-base assistance of His194. Residue Arg249 has an important role in the ability of the enzyme to bind the glyceraldehyde 3-phosphatesubstrate, which interacts with NAD+ and other important residues, such as Cys166, Glu109, Thr167, Ser247 and Thr226, in the GAPDH active site