Literature summary for 1.2.1.12 extracted from

Tien, Y.C.; Chuankhayan, P.; Huang, Y.C.; Chen, C.D.; Alikhajeh, J.; Chang, S.L.; Chen, C.J.
Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37 in NAD binding for catalysis (2012), Plant Mol. Biol., 80, 389-403.

Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Escherichia coli JM109 cells	Oryza sativa

Crystallization (Commentary)

Crystallization (Comment)	Organism
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)	Oryza sativa
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	Oryza sativa Japonica Group

Crystallization (Comment)

Organism

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)

Oryza sativa

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

Oryza sativa Japonica Group

Protein Variants

Protein Variants	Comment	Organism
F37G	the mutant shows strongly reduced kcat values compared to the wild type enzyme	Oryza sativa
F37G	substitution of residue F37 with Gly, Thr or Leu leads to 6- to 9fold increase in Km value for cofactor NAD+ or NADG, with only slight increase for substrates D- glyceraldehyde 3-phosphate or 3-phospho-D-glyceroyl phosphate	Oryza sativa Japonica Group
F37L	the mutant shows strongly reduced kcat values compared to the wild type enzyme	Oryza sativa
F37L	substitution of residue F37 with Gly, Thr or Leu leads to 6- to 9fold increase in Km value for cofactor NAD+ or NADG, with only slight increase for substrates D-glyceraldehyde 3-phosphate or 3-phospho-D-glyceroyl phosphate	Oryza sativa Japonica Group
F37T	the mutant shows strongly reduced kcat values compared to the wild type enzyme	Oryza sativa
F37T	substitution of residue F37 with Gly, Thr or Leu leads to 6- to 9fold increase in Km value for cofactor NAD+ or NADG, with only slight increase for substrates D-glyceraldehyde 3-phosphate or 3-phospho-D-glyceroyl phosphate	Oryza sativa Japonica Group

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.036	-	3-phospho-D-glyceroyl phosphate	wild type enzyme, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.036	-	3-phospho-D-glyceroyl phosphate	wild-type, pH 8.8, 25°C	Oryza sativa Japonica Group
0.049	-	3-phospho-D-glyceroyl phosphate	mutant enzyme F37L, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.049	-	3-phospho-D-glyceroyl phosphate	mutant F36L, pH 8.8, 25°C	Oryza sativa Japonica Group
0.051	-	3-phospho-D-glyceroyl phosphate	mutant enzyme F37G, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.051	-	3-phospho-D-glyceroyl phosphate	mutant F36G, pH 8.8, 25°C	Oryza sativa Japonica Group
0.053	-	3-phospho-D-glyceroyl phosphate	mutant enzyme F37T, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.053	-	3-phospho-D-glyceroyl phosphate	mutant F36T, pH 8.8, 25°C	Oryza sativa Japonica Group
0.059	-	NAD+	wild type enzyme, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.059	-	NAD+	wild-type, pH 8.8, 25°C	Oryza sativa Japonica Group
0.061	-	NADH	wild type enzyme, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.061	-	NADH	wild-type, pH 8.8, 25°C	Oryza sativa Japonica Group
0.111	-	D-glyceraldehyde 3-phosphate	wild type enzyme, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.111	-	D-glyceraldehyde 3-phosphate	wild-type, pH 8.8, 25°C	Oryza sativa Japonica Group
0.149	-	D-glyceraldehyde 3-phosphate	mutant enzyme F37L, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.149	-	D-glyceraldehyde 3-phosphate	mutant F36L, pH 8.8, 25°C	Oryza sativa Japonica Group
0.156	-	D-glyceraldehyde 3-phosphate	mutant enzyme F37G, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.156	-	D-glyceraldehyde 3-phosphate	mutant F36G, pH 8.8, 25°C	Oryza sativa Japonica Group
0.161	-	D-glyceraldehyde 3-phosphate	mutant enzyme F37T, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.161	-	D-glyceraldehyde 3-phosphate	mutant F36T, pH 8.8, 25°C	Oryza sativa Japonica Group
0.362	-	NAD+	mutant enzyme F37G, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.362	-	NAD+	mutant F36G, pH 8.8, 25°C	Oryza sativa Japonica Group
0.367	-	NADH	mutant enzyme F37G, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.367	-	NADH	mutant F36G, pH 8.8, 25°C	Oryza sativa Japonica Group
0.403	-	NADH	mutant enzyme F37T, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.403	-	NADH	mutant F36T, pH 8.8, 25°C	Oryza sativa Japonica Group
0.417	-	NAD+	mutant enzyme F37T, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.417	-	NAD+	mutant F36T, pH 8.8, 25°C	Oryza sativa Japonica Group
0.527	-	NAD+	mutant enzyme F37L, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.527	-	NAD+	mutant F36L, pH 8.8, 25°C	Oryza sativa Japonica Group
0.537	-	NADH	mutant enzyme F37L, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.537	-	NADH	mutant F36L, pH 8.8, 25°C	Oryza sativa Japonica Group

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
cytosol	-	Oryza sativa Japonica Group	5829	-

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
37000	-	4 * 37000, SDS-PAGE	Oryza sativa

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
3-phospho-D-glyceroyl phosphate + NADH + H+	Oryza sativa	-	D-glyceraldehyde 3-phosphate + phosphate + NAD+	-	r
D-glyceraldehyde 3-phosphate + phosphate + NAD+	Oryza sativa	-	3-phospho-D-glyceroyl phosphate + NADH + H+	-	r
additional information	Oryza sativa	no activity with NADP+	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Oryza sativa	Q0J8A4	-	-
Oryza sativa Japonica Group	Q0J8A4	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
3-phospho-D-glyceroyl phosphate + NADH	-	Oryza sativa Japonica Group	D-glyceraldehyde 3-phosphate + phosphate + NAD+	-	r
3-phospho-D-glyceroyl phosphate + NADH + H+	-	Oryza sativa	D-glyceraldehyde 3-phosphate + phosphate + NAD+	-	r
D-glyceraldehyde 3-phosphate + phosphate + NAD+	-	Oryza sativa Japonica Group	3-phospho-D-glyceroyl phosphate + NADH	-	r
D-glyceraldehyde 3-phosphate + phosphate + NAD+	-	Oryza sativa	3-phospho-D-glyceroyl phosphate + NADH + H+	-	r
additional information	no activity with NADP+	Oryza sativa	?	-	?

Subunits

Subunits	Comment	Organism
homotetramer	4 * 37000, SDS-PAGE	Oryza sativa

Synonyms

Synonyms	Comment	Organism
GAPDH	-	Oryza sativa

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.06	-	3-phospho-D-glyceroyl phosphate	mutant enzyme F37L, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.06	-	NADH	mutant F36L, pH 8.8, 25°C	Oryza sativa Japonica Group
0.08	-	3-phospho-D-glyceroyl phosphate	mutant enzyme F37T, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.08	-	NADH	mutant F36T, pH 8.8, 25°C	Oryza sativa Japonica Group
0.09	-	D-glyceraldehyde 3-phosphate	mutant enzyme F37L, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.09	-	NAD+	mutant F36L, pH 8.8, 25°C	Oryza sativa Japonica Group
0.13	-	D-glyceraldehyde 3-phosphate	mutant enzyme F37T, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.13	-	NAD+	mutant F36T, pH 8.8, 25°C	Oryza sativa Japonica Group
0.14	-	3-phospho-D-glyceroyl phosphate	mutant enzyme F37G, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
0.14	-	NADH	mutant F36G, pH 8.8, 25°C	Oryza sativa Japonica Group
0.24	-	D-glyceraldehyde 3-phosphate	mutant enzyme F37G, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa
0.24	-	NAD+	mutant F36G, pH 8.8, 25°C	Oryza sativa Japonica Group
73.56	-	3-phospho-D-glyceroyl phosphate	wild type enzyme, in 80 mM triethanolamine, 3.3 mM L-cysteine HCl, 1.7 mM MgSO4, 0.5 mM EDTA, pH 7.6, at 25°C	Oryza sativa
73.6	-	NADH	wild-type, pH 8.8, 25°C	Oryza sativa Japonica Group
122	-	NAD+	wild-type, pH 8.8, 25°C	Oryza sativa Japonica Group
122.2	-	D-glyceraldehyde 3-phosphate	wild type enzyme, in 50 mM triethanolamine, 50 mM Na2HPO4, 0.2 mM EDTA, at pH 8.8 and 25°C	Oryza sativa

Cofactor

Cofactor	Comment	Organism	Structure
additional information	no activity with NADP+ or NADPH	Oryza sativa Japonica Group
NAD+	-	Oryza sativa