Information on EC 1.4.1.7 - serine 2-dehydrogenase

for references in articles please use BRENDA:EC1.4.1.7
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

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EC NUMBER
COMMENTARY hide
1.4.1.7
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RECOMMENDED NAME
GeneOntology No.
serine 2-dehydrogenase
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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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-
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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-
-
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oxidative deamination
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-
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reduction
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-
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reductive amination redox reaction
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-
-
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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
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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
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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
-
-
?
(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
-
-
-
-
?
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
-
-
?
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
-
-
-
-
-
L-serine + H2O + NAD+
3-hydroxypyruvate + NH3 + NADH + H+
show the reaction diagram
-
-
-
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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
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
p-chloromercurybenzoate
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completely inhibited at 0.005 mM
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.4
3-methyl-DL-serine
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
19.8
DL-glycerate
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
0.0005
Hydroxypyruvate
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2.5
L-serine
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
17.4
methyl 2,2-dimethyl-3-hydroxypropionic acid
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
3.4
NAD+
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9.6
3-methyl-DL-serine
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
5.8
DL-glycerate
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
10.4
L-serine
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
11.6
methyl 2,2-dimethyl-3-hydroxypropionic acid
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
1.6
NAD+
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
40
3-methyl-DL-serine
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
0.3
DL-glycerate
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
40
L-serine
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
0.7
methyl 2,2-dimethyl-3-hydroxypropionic acid
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
0.5
NAD+
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pH 11.0, 37°C, recombinant His-tagged wild-type enzyme
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10
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in phosphate buffer
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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green leaves
Manually annotated by BRENDA team
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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
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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
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LINKS TO OTHER DATABASES (specific for EC-Number 1.4.1.7)
ExplorEnz
ExPASy
KEGG
MetaCyc
SABIO-RK
NCBI: PubMed, Protein, Nucleotide, Structure, Genome, OMIM
IUBMB Enzyme Nomenclature
PROSITE Database of protein families and domains
InterPro (database of protein families, domains and functional sites)