The enzyme, purified from the bacterium Pseudomonas aeruginosa, also shows activity with L-threonine (cf. EC 1.1.1.103, L-threonine 3-dehydrogenase). The enzyme has only very low activity with NADP+ [cf. EC 1.1.1.276, serine 3-dehydrogenase (NADP+)].
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The expected taxonomic range for this enzyme is: Bacteria, Archaea
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SYSTEMATIC NAME
IUBMB Comments
L-serine:NAD+ 3-oxidoreductase
The enzyme, purified from the bacterium Pseudomonas aeruginosa, also shows activity with L-threonine (cf. EC 1.1.1.103, L-threonine 3-dehydrogenase). The enzyme has only very low activity with NADP+ [cf. EC 1.1.1.276, serine 3-dehydrogenase (NADP+)].
modeling of the D-serine and 3-hydroxypropionate molecules into the enzyme's active site. No steric hindrance is observed between D-serine and the side chains of the active site residues. D-serine is placed at the position through interactions similar to the L-serine binding model. The C3 hydrogen of D-serine is located at the same position as that of L-serine. This may explain the high reactivity toward D-serine exhibited by Pyrobaculum calidifontis L-SerDH
the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases
the enzyme might be involved in serine/methylserine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases
the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases
both NAD+ and NADP+ are capable of serving as cofactors for the enzyme, but the reaction rate with NADP+ is 7.9% of that observed with NAD+ with L-serine as substrate. Deamido-NAD+ is not able to serve as cofactor. Cofactor binding mechanism, overview
the enzyme activity is unaffected by 1 mM of EDTA, LiSO4, MgCl2, MnCl2, CaCl2, NiCl2, CoCl2, BaCl2, CuSO4, ZnCl2, iodoacetic acid, and L-(+)-tartaric acid
the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases
L-serine 3-dehydrogenase acts at the beta-carbon (C3) position of L-serine. The product of this reaction is supposed to be 2-aminomalonate semialdehyde, which nonenzymatically decomposes into 2-aminoacetaldehyde and CO2
catalytic domain fold of the Pyrobaculum calidifontis enzyme shows similarity with that of Pseudomonas aeruginosa L-SerDH, but the active site structure significantly differs between the two enzymes. Based on the structure of the tartrate, L- and D-serine and 3-hydroxypropionate molecules are modeled into the active site and the substrate binding modes are estimated. The wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both L- and D-serine enantiomers. Analysis of the substrate binding mechanism of L-SerDH, and detailed enzyme structure analysis, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
two crystal structures of the enzyme are solved at 2.2-2.3 A resolution and reveal an N-terminal Rossmann fold domain connected by a long alpha-helix to the C-terminal all-alpha-domain. The apostructure shows the presence of additional density modeled as HEPES bound in the interdomain cleft close to the predicted catalytic Lys171, revealing the molecular details of the enzyme substrate-binding site. The structure of the enzyme-NAD complex demonstrates that the opposite side of the enzyme active site accommodates the cofactor, which is also bound near Lys171. Crystals of the enzyme are grown at 21C by the hanging drop vapor diffusion method with 0.002 ml of protein sample mixed with an equal volume of the reservoir buffer. The crystals of the wild-type enzyme grew after 1 week in the presence of 4 M ammonium acetate and 0.1 M sodium acetate (pH 5.4). The crystals of the complex of the enzyme with NAD+ are obtained by soaking the crystals in 10 mM NAD+. For diffraction studies, the crystals are stabilized with the crystallization buffer supplemented with 12% ethylene glycol as a cryoprotectant and flash frozen in liquid nitrogen
purified recombinant wild-type and mutant enzymes in complex with NADP+/sulfate ion and with NADP+/L-tartrate (substrate analogue), sitting-drop vapor diffusion method, mixing of 0.001 ml of 13 mg/mL protein in 10 mM Tris-HCl, pH 8.0, 200 mM NaCl, and 5 mM 2-mercaptoethanol, with 0.001 ml of mother liquor containing 30% w/v PEG 2000 MME, 0.2 M ammonium sulfate, and 100 mM acetate buffer, pH 4.6, for complex crystals 0.5 mM NADP+ is added to the protein solution, soaking of the crystals in mother liquor containing 0.45 M L-(+)-tartaric acid for 10 min, X-ray diffraction structure determination and analysis at 1.18 and 1.57 A resolution, respectively. Based on the model of the selenomethionyl enzyme (PDB entry, 3W6U), the structure of the NADP+/ sulfate ion-bound and NADP+/ tartrate-bound enzymes is determined using the molecular replacement method, modeling
recombinant His-tagged and selenomethionyl-labeled wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) codon plus RIPL by nickel affinity chromatography, removal of the first 17 amino acids of the N-terminal region of the His-tagged enzyme by thrombin
recombinant overexpression of His-tagged and selenomethionyl-labeled wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) codon plus RIPL, expression of the enzyme from the L-SerDH-pET-15b plasmid (pET0699) in a modified M9 medium containing selenomethionine