Information on EC 1.4.1.7 - serine 2-dehydrogenase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.4.1.7
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RECOMMENDED NAME
GeneOntology No.
serine 2-dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-serine + H2O + NAD+ = 3-hydroxypyruvate + NH3 + NADH + H+
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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oxidative deamination
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-
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reduction
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reductive amination redox reaction
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SYSTEMATIC NAME
IUBMB Comments
L-serine:NAD+ 2-oxidoreductase (deaminating)
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CAS REGISTRY NUMBER
COMMENTARY hide
9038-55-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
the enzyme has an N-terminal Rossmann fold domain connected by a long alpha-helix to the C-terminal all-alpha domain. Critical role of four amino acid residues in catalysis including the primary catalytic residue Lys171, PA0743 substrate-binding site structure and molecular mechanisms of substrate selectivity, overview. The structure of the PA0743-NAD+ complex demonstrates that the opposite side of the enzyme active site accommodates the cofactor, which is also bound near Lys171
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(R)-3-hydroxyisobutyric acid + H2O + NAD+
? + NH3 + NADH + H+
show the reaction diagram
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low activity
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-
?
(S)-3-hydroxyisobutyric acid + H2O + NAD+
? + NH3 + NADH + H+
show the reaction diagram
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low activity
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-
?
3-methyl-DL-serine + H2O + NAD+
2-aminomethylmalonate semialdehyde + NH3 + NADH + H+
show the reaction diagram
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high activity
-
-
?
D-serine + H2O + NAD+
3-hydroxypyruvate + NH3 + NADH + H+
show the reaction diagram
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low activity
-
-
?
DL-glycerate + H2O + NAD+
? + NH3 + NADH + H+
show the reaction diagram
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low activity
-
-
?
L-serine + H2O + NAD+
3-hydroxypyruvate + NH3 + NADH
show the reaction diagram
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-
-
-
?
L-serine + H2O + NAD+
3-hydroxypyruvate + NH3 + NADH + H+
show the reaction diagram
methyl (R)-3-hydroxy-2-methylpropionic acid + H2O + NAD+
? + NH3 + NADH + H+
show the reaction diagram
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low activity
-
-
?
methyl (S)-3-hydroxy-2-methylpropionic acid + H2O + NAD+
? + NH3 + NADH + H+
show the reaction diagram
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low activity
-
-
?
methyl 2,2-dimethyl-3-hydroxypropionic acid + H2O + NAD+
? + NH3 + NADH + H+
show the reaction diagram
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low activity
-
-
?
tert-butyl 3-hydroxypropionic acid + H2O + NAD+
? + NH3 + NADH + H+
show the reaction diagram
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low activity
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-serine + H2O + NAD+
3-hydroxypyruvate + NH3 + NADH
show the reaction diagram
-
-
-
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L-serine + H2O + NAD+
3-hydroxypyruvate + NH3 + NADH + H+
show the reaction diagram
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-
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?
additional information
?
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PA0743 from Pseudomonas aeruginosa catalyzes NAD-dependent oxidation of L-serine and methyl-L-serine, and exhibits low activity against beta-hydroxyisobutyrate
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NAD+
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binding GLGXMG motif-1 and motif-4, the nicotinamide moiety of NAD+ is mostly buried in the interdomain cleft of the PA0743 protomer
NADH
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specific for NADH, does not react with NADPH, strictly specific for hydroxypyruvate in presence of NADH
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
p-chloromercurybenzoate
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completely inhibited at 0.005 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.4
3-methyl-DL-serine
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
19.8
DL-glycerate
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
0.0005
Hydroxypyruvate
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2.5
L-serine
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
17.4
methyl 2,2-dimethyl-3-hydroxypropionic acid
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
3.4
NAD+
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9.6
3-methyl-DL-serine
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
5.8
DL-glycerate
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
10.4
L-serine
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
11.6
methyl 2,2-dimethyl-3-hydroxypropionic acid
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
1.6
NAD+
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
40
3-methyl-DL-serine
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
42621
0.3
DL-glycerate
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
5238
40
L-serine
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
95
0.7
methyl 2,2-dimethyl-3-hydroxypropionic acid
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
42622
0.5
NAD+
Pseudomonas aeruginosa
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pH 11.0, 37C, recombinant His-tagged wild-type enzyme
7
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10
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in phosphate buffer
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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green leaves
Manually annotated by BRENDA team
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
the enzyme has an N-terminal Rossmann fold domain connected by a long alpha-helix to the C-terminal all-alpha domain. Critical role of four amino acid residues in catalysis including the primary catalytic residue Lys171, PA0743 substrate-binding site structure, and molecular mechanisms of substrate selectivity, overview. The structure of the PA0743-NAD+ complex demonstrates that the opposite side of the enzyme active site accommodates the cofactor, which is also bound near Lys171, with dinucleotide cofactor binding GLGXMG motif-1, substrate binding DAPVSGG motif-2, catalysis GXXGXGXXXKXXN motif-3, and cofactor binding motif-4
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified His-tagged recombinant protein PA0743 alone or in complex with cofactor NAD+, hanging drop vapor diffusion method, mixing of 0.002 ml protein solution with 0.002 ml reservoir solution containing 4 M ammonium acetate and 0.1 M sodium acetate, at pH 5.4, 1 week, soaking of crystals in 10 mM NAD+ solution for complexcystals, X-ray diffraction structure determination and analysis at 2.2 A resolution
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
very labile enzyme, loses its activity when exposed to dialysis or weak heating
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
isolated from an albumin fraction, purified on Sephadex G-76, subsequently on DEAE-cellulose
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recombinant wild-type and mutant His-tagged enzymes from Escherichia coli strain BL21(DE3) Gold by nickel affinity chromatography and gel filtration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
PA0743 open reading frame, expression of wild-type and mutant His-tagged enzymes in Escherichia coli strain BL21(DE3) Gold
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D247A
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site-directed mutagenesis, inactive mutant
E122A
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site-directed mutagenesis, the mutant shows alterations in cofactor binding and highly reduced activity compared to the wild-type enzyme
K171A
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site-directed mutagenesis, inactive mutant
K246A
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site-directed mutagenesis, inactive mutant
N175A
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site-directed mutagenesis, the mutant shows alterations in cofactor binding and highly reduced activity compared to the wild-type enzyme
T96A
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site-directed mutagenesis, the mutant shows alterations in cofactor binding and highly reduced activity compared to the wild-type enzyme
W214A
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site-directed mutagenesis, inactive mutant
Y219A
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site-directed mutagenesis, the mutant shows alterations in cofactor binding and highly reduced activity compared to the wild-type enzyme
additional information
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PA0743 deletion (PW2350) strain from a transposon library