BRENDA - Enzyme Database

Crystal structure of D-erythronate-4-phosphate dehydrogenase complexed with NAD

Ha, J.Y.; Lee, J.H.; Kim, K.H.; Kim, d.o..J.; Lee, H.H.; Kim, H.K.; Yoon, H.J.; Suh, S.W.; J. Mol. Biol. 366, 1294-1304 (2007)

Data extracted from this reference:

Crystallization (Commentary)
EC Number
Crystallization
Organism
1.1.1.290
purified recombinant C-terminally His8-tagged and selenomethionine-labeled enzyme, subunit A is bound with NAD+ and a phosphate ion, while subunit B, with a more open active site cleft, is bound with NAD+ and L(+)-tartrate, cryoprotection by 30% glycerol, X-ray diffraction structure determination and analysis at 2.3 A resolution, asymmetric subunit conformation and strucure comparison, overview
Pseudomonas aeruginosa
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.290
4-phospho-D-erythronate + NAD+
Pseudomonas aeruginosa
the enzyme is involved in biosynthesis of pyridoxal-5'-phosphate
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.290
Pseudomonas aeruginosa
Q9I3W9
gene pdxB
-
Reaction
EC Number
Reaction
Commentary
Organism
1.1.1.290
4-phospho-D-erythronate + NAD+ = (3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH + H+
substrate recognition and catalytic mechanism, PdxB contains the conserved His254/Glu237/Arg208 triad
Pseudomonas aeruginosa
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.290
4-phospho-D-erythronate + NAD+
-
688340
Pseudomonas aeruginosa
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
the enzyme is involved in biosynthesis of pyridoxal-5'-phosphate
688340
Pseudomonas aeruginosa
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
-
-
-
?
1.1.1.290
additional information
active site and ligand binding structure, overview
688340
Pseudomonas aeruginosa
?
-
-
-
-
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.290
dimer
homodimer, each subunit consists of three structural domains: the lid domain, the nucleotide-binding domain, and the C-terminal dimerization domain with a unique fold responsible for the dimerization, crystal structure analysis, overview
Pseudomonas aeruginosa
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.290
NAD+
NAD+ is bound to the C-terminal side of the beta-sheet of the nucleotide-binding domain in both subunits of PdxB, binding structure, overview
Pseudomonas aeruginosa
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.290
NAD+
NAD+ is bound to the C-terminal side of the beta-sheet of the nucleotide-binding domain in both subunits of PdxB, binding structure, overview
Pseudomonas aeruginosa
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.1.1.290
purified recombinant C-terminally His8-tagged and selenomethionine-labeled enzyme, subunit A is bound with NAD+ and a phosphate ion, while subunit B, with a more open active site cleft, is bound with NAD+ and L(+)-tartrate, cryoprotection by 30% glycerol, X-ray diffraction structure determination and analysis at 2.3 A resolution, asymmetric subunit conformation and strucure comparison, overview
Pseudomonas aeruginosa
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.290
4-phospho-D-erythronate + NAD+
Pseudomonas aeruginosa
the enzyme is involved in biosynthesis of pyridoxal-5'-phosphate
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
-
-
?
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.290
4-phospho-D-erythronate + NAD+
-
688340
Pseudomonas aeruginosa
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
-
-
-
?
1.1.1.290
4-phospho-D-erythronate + NAD+
the enzyme is involved in biosynthesis of pyridoxal-5'-phosphate
688340
Pseudomonas aeruginosa
(3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH
-
-
-
?
1.1.1.290
additional information
active site and ligand binding structure, overview
688340
Pseudomonas aeruginosa
?
-
-
-
-
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.290
dimer
homodimer, each subunit consists of three structural domains: the lid domain, the nucleotide-binding domain, and the C-terminal dimerization domain with a unique fold responsible for the dimerization, crystal structure analysis, overview
Pseudomonas aeruginosa