BRENDA - Enzyme Database

Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism

Yeh, J.I.; Chinte, U.; Du, S.; Proc. Natl. Acad. Sci. USA 105, 3280-3285 (2008)

Data extracted from this reference:

Crystallization (Commentary)
EC Number
Crystallization
Organism
1.1.1.8
purified GlpD is concentrated to 8 mg/ml and crystallized at 4°C from a solution containing 0.1 M diammonium hydrogen phosphate, 0.1 M Bicine pH 8.5, and 12% w/v PEG 6000. Structure of the native enzyme, structures of enzyme complexed with substrate analogues phosphoenolpyruvate, glyceric acid 2-phosphate, glyceraldehyde-3-phosphate, and product, dihydroxyacetone phosphate
Escherichia coli
1.1.1.94
crystal structure analysis: GlpD comprises two major domains, a soluble extramembraneous C-terminal cap domain (residues 389-501) and a N-terminal FAD-binding region, consisting of the substrate binding and base regions (residues 1-388). The dimeric enzyme is formed by monomers related by a noncrystallographic 2fold axis of symmetry and the dimer comprises the unique asymmetric unit. Electrostatic surface calculations show distinct regions of highly positive patches, located at the base region of the enzyme. These regions are likely involved with the negatively charged membrane phospholipid head groups. The cap domain, at the opposite side, exhibits highly negatively electrostatic potential, with large hydrophobic patches between these two distal regions of the enzyme, forming membrane interaction and proposed UQ-binding surfaces; structure of the native enzyme and in complex with dihydroxyacetone phosphate (2.1 A) and in separate complexes with substrate analogues, glyceraldehyde-3-phosphate (2.9 A), glyceric acid 2-phosphate (2.3 A), and phosphoenolpyruvate (2.1 A) are determined. Additionally, in complex with ubiquinone analogues, menadione (2.6 A) and 2-n-heptyl-4-hydroxyquinoline N-oxide (2.9 A)
Escherichia coli
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.94
glyceraldehyde-3-phosphate
competitive inhibitor
Escherichia coli
1.1.1.94
glyceric acid 2-phosphate
competitive inhibitor
Escherichia coli
1.1.1.94
phosphoenolpyruvate
competitive inhibitor
Escherichia coli
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.8
Escherichia coli
-
-
-
1.1.1.94
Escherichia coli
P13035
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.8
-
Escherichia coli
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.94
glyceraldehyde-3-phosphate + NAD(P)+
crystal structure with complexed substrate analogue is determined
689802
Escherichia coli
?
-
-
-
?
1.1.1.94
glyceric acid 2-phosphate + NAD(P)+
crystal structure with complexed substrate analogue is determined
689802
Escherichia coli
?
-
-
-
?
1.1.1.94
phosphoenolpyruvate + NAD(P)+
crystal structure with complexed substrate analogue is determined
689802
Escherichia coli
?
-
-
-
?
1.1.1.94
sn-glycerol 3-phosphate + NAD(P)+
-
689802
Escherichia coli
glycerone phosphate + NAD(P)H + H+
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.94
dimer
crystal structure
Escherichia coli
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.94
FAD
-
Escherichia coli
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.94
FAD
-
Escherichia coli
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.1.1.8
purified GlpD is concentrated to 8 mg/ml and crystallized at 4°C from a solution containing 0.1 M diammonium hydrogen phosphate, 0.1 M Bicine pH 8.5, and 12% w/v PEG 6000. Structure of the native enzyme, structures of enzyme complexed with substrate analogues phosphoenolpyruvate, glyceric acid 2-phosphate, glyceraldehyde-3-phosphate, and product, dihydroxyacetone phosphate
Escherichia coli
1.1.1.94
crystal structure analysis: GlpD comprises two major domains, a soluble extramembraneous C-terminal cap domain (residues 389-501) and a N-terminal FAD-binding region, consisting of the substrate binding and base regions (residues 1-388). The dimeric enzyme is formed by monomers related by a noncrystallographic 2fold axis of symmetry and the dimer comprises the unique asymmetric unit. Electrostatic surface calculations show distinct regions of highly positive patches, located at the base region of the enzyme. These regions are likely involved with the negatively charged membrane phospholipid head groups. The cap domain, at the opposite side, exhibits highly negatively electrostatic potential, with large hydrophobic patches between these two distal regions of the enzyme, forming membrane interaction and proposed UQ-binding surfaces; structure of the native enzyme and in complex with dihydroxyacetone phosphate (2.1 A) and in separate complexes with substrate analogues, glyceraldehyde-3-phosphate (2.9 A), glyceric acid 2-phosphate (2.3 A), and phosphoenolpyruvate (2.1 A) are determined. Additionally, in complex with ubiquinone analogues, menadione (2.6 A) and 2-n-heptyl-4-hydroxyquinoline N-oxide (2.9 A)
Escherichia coli
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.94
glyceraldehyde-3-phosphate
competitive inhibitor
Escherichia coli
1.1.1.94
glyceric acid 2-phosphate
competitive inhibitor
Escherichia coli
1.1.1.94
phosphoenolpyruvate
competitive inhibitor
Escherichia coli
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.8
-
Escherichia coli
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.94
glyceraldehyde-3-phosphate + NAD(P)+
crystal structure with complexed substrate analogue is determined
689802
Escherichia coli
?
-
-
-
?
1.1.1.94
glyceric acid 2-phosphate + NAD(P)+
crystal structure with complexed substrate analogue is determined
689802
Escherichia coli
?
-
-
-
?
1.1.1.94
phosphoenolpyruvate + NAD(P)+
crystal structure with complexed substrate analogue is determined
689802
Escherichia coli
?
-
-
-
?
1.1.1.94
sn-glycerol 3-phosphate + NAD(P)+
-
689802
Escherichia coli
glycerone phosphate + NAD(P)H + H+
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.94
dimer
crystal structure
Escherichia coli