Literature summary for 1.1.1.387 extracted from

Yoneda, K.; Sakuraba, H.; Araki, T.; Ohshima, T.
Crystal structure of the NADP+ and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis (2018), Extremophiles, 22, 395-405 .

Search for more literature for 1.1.1.387

Activating Compound

Activating Compound	Comment	Organism	Structure
additional information	the enzyme activity is unaffected by 1 mM of EDTA, iodoacetic acid, and L-(+)-tartaric acid	Pyrobaculum calidifontis

Cloned(Commentary)

Cloned (Comment)	Organism
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	Pyrobaculum calidifontis

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Pyrobaculum calidifontis

Crystallization (Comment)

Organism

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

Pyrobaculum calidifontis

Protein Variants

Protein Variants	Comment	Organism
K170M	site-directed mutagenesis	Pyrobaculum calidifontis

Inhibitors

Inhibitors	Comment	Organism
CdSO4	21% inhibition at 1 mM	Pyrobaculum calidifontis
D-cysteine	59.2% inhibition at 1 mM	Pyrobaculum calidifontis
HgCl2	31.6% inhibition at 1 mM	Pyrobaculum calidifontis
L-cysteine	53.3% inhibition at 1 mM	Pyrobaculum calidifontis
additional information	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	Pyrobaculum calidifontis
NADP+	92.2% inhibition at 1 mM	Pyrobaculum calidifontis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
additional information	-	additional information	Michaelis-Menten type kinetics	Pyrobaculum calidifontis
0.033	-	NADP+	pH 10.0, 50°C, recombinant wild-type enzyme	Pyrobaculum calidifontis
0.38	-	NAD+	pH 10.0, 50°C, recombinant wild-type enzyme	Pyrobaculum calidifontis
2.16	-	DL-glycerate	pH 10.0, 50°C, recombinant wild-type enzyme	Pyrobaculum calidifontis
4.33	-	L-serine	pH 10.0, 50°C, recombinant wild-type enzyme	Pyrobaculum calidifontis
6.09	-	D-serine	pH 10.0, 50°C, recombinant wild-type enzyme	Pyrobaculum calidifontis
34.57	-	DL-3-hydroxyisobutyrate	pH 10.0, 50°C, recombinant wild-type enzyme	Pyrobaculum calidifontis
69.04	-	3-hydroxypropionate	pH 10.0, 50°C, recombinant wild-type enzyme	Pyrobaculum calidifontis

Metals/Ions

Metals/Ions	Comment	Organism	Structure
additional information	the enzyme activity is unaffected by 1 mM of LiSO4, MgCl2, MnCl2, CaCl2, NiCl2, CoCl2, BaCl2, CuSO4, and ZnCl2	Pyrobaculum calidifontis

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
51000	-	recombinant enzyme, gel filtration	Pyrobaculum calidifontis

Organism

Organism	UniProt	Comment	Textmining
Pyrobaculum calidifontis	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
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	Pyrobaculum calidifontis

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
3.48	-	purified recombinant wild-type enzyme, pH 10.0, 50°C	Pyrobaculum calidifontis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
2-aminomalonate semialdehyde	spontaneous	Pyrobaculum calidifontis	2-aminoacetaldehyde + CO2	-	?
3-hydroxypropionate + NAD+	-	Pyrobaculum calidifontis	? + NADH + H+	-	?
D-serine + NAD+	overall reaction, 5% of the relative activity observed with L-serine	Pyrobaculum calidifontis	2-aminoacetaldehyde + CO2 + NADH + H+	-	?
DL-3-hydroxyisobutyrate + NAD+	-	Pyrobaculum calidifontis	? + NADH + H+	-	?
DL-glycerate + NAD+	-	Pyrobaculum calidifontis	? + NADH + H+	-	?
L-serine + NAD(P)+	-	Pyrobaculum calidifontis	2-aminomalonate semialdehyde + NAD(P)H + H+	-	?
L-serine + NAD+	overall reaction, NAD+ is the preferred cofactor	Pyrobaculum calidifontis	2-aminoacetaldehyde + CO2 + NADH + H+	-	?
L-serine + NADP+	overall reaction, low activity with NADP+	Pyrobaculum calidifontis	2-aminoacetaldehyde + CO2 + NADPH + H+	-	?
additional information	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	Pyrobaculum calidifontis	?	-	-

Subunits

Subunits	Comment	Organism
homodimer	2 * 27000, recombinant enzyme, SDS-PAGE	Pyrobaculum calidifontis

Synonyms

Synonyms	Comment	Organism
L-SerDH	-	Pyrobaculum calidifontis
L-serine 3-dehydrogenase	-	Pyrobaculum calidifontis
L-serine dehydrogenase	-	Pyrobaculum calidifontis

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
50	-	assay at	Pyrobaculum calidifontis

Temperature Stability [°C]

Temperature Stability Minimum [°C]	Temperature Stability Maximum [°C]	Comment	Organism
100	-	recombinant enzyme, no loss of activity is observed by incubation for 30 min at temperatures up to 100°C	Pyrobaculum calidifontis

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
10	-	assay at	Pyrobaculum calidifontis

Cofactor

Cofactor	Comment	Organism
additional information	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	Pyrobaculum calidifontis
NAD+	-	Pyrobaculum calidifontis
NADH	-	Pyrobaculum calidifontis
NADP+	-	Pyrobaculum calidifontis
NADPH	-	Pyrobaculum calidifontis

General Information

General Information	Comment	Organism
additional information	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	Pyrobaculum calidifontis
physiological function	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	Pyrobaculum calidifontis