Information on EC 4.3.1.17 - L-serine ammonia-lyase

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

EC NUMBER
COMMENTARY hide
4.3.1.17
-
RECOMMENDED NAME
GeneOntology No.
L-serine ammonia-lyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-aminoprop-2-enoate = 2-iminopropanoate
show the reaction diagram
(1b), spontaneous
-
-
-
2-iminopropanoate + H2O = pyruvate + NH3
show the reaction diagram
(1c), spontaneous
-
-
-
L-serine = 2-aminoprop-2-enoate + H2O
show the reaction diagram
(1a)
-
-
-
L-serine = pyruvate + NH3
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
alpha,beta-position of amino acid; beta-position of amino acid; of NH3, alpha,beta-position of amino acid; of NH3, alpha,beta-position of amino acid, C-N bond cleavage, C-O bond cleavage
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
Cysteine and methionine metabolism
-
-
Glycine, serine and threonine metabolism
-
-
Metabolic pathways
-
-
purine metabolism
-
-
serine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
L-serine ammonia-lyase (pyruvate-forming)
Most enzymes that catalyse this reaction are pyridoxal-phosphate-dependent, although some enzymes contain an iron-sulfur cluster instead [6]. The reaction catalysed by both types of enzymes involves the initial elimination of water to form an enamine intermediate (hence the enzyme's original classification as EC 4.2.1.13, L-serine dehydratase), followed by tautomerization to an imine form and hydrolysis of the C-N bond. The latter reaction, which can occur spontaneously, is also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. This reaction is also carried out by EC 4.3.1.19, threonine ammonia-lyase, from a number of sources.
CAS REGISTRY NUMBER
COMMENTARY hide
9014-27-1
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
NRRL3
-
-
Manually annotated by BRENDA team
NRRL3
-
-
Manually annotated by BRENDA team
DSM 826
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Clostridium acidi-urici
-
-
-
Manually annotated by BRENDA team
strain AJ-3170 and various mutants
-
-
Manually annotated by BRENDA team
strain AJ-3170 and various mutants
-
-
Manually annotated by BRENDA team
three genes sdaA, sdaB, tdcG encoding the isozymes of SDH
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain DL-1, ATCC 51573, gene GSU0486 or tcdB
-
-
Manually annotated by BRENDA team
strain DL-1, ATCC 51573, gene GSU0486 or tcdB
-
-
Manually annotated by BRENDA team
strain CNRZ 313
-
-
Manually annotated by BRENDA team
strain CNRZ 313
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
NRC-510
-
-
Manually annotated by BRENDA team
NRC-510
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
beta-chloro-L-alanine
3-chloropropenoic acid + NH3
show the reaction diagram
-
-
-
?
D-serine
L-serine
show the reaction diagram
D-serine
pyruvate + NH3
show the reaction diagram
L-allo-threonine
2-oxobutyrate + NH3
show the reaction diagram
-
at 4.6% of the rate with L-serine
-
-
?
L-Leu
3-Hydroxy-2-oxopropionate + NH3
show the reaction diagram
L-Ser
?
show the reaction diagram
L-Ser
pyruvate + NH3
show the reaction diagram
-
-
-
ir
L-serine
D-serine
show the reaction diagram
L-serine
pyruvate + NH3
show the reaction diagram
L-serine O-sulfate
O-sulfopyruvate + NH3
show the reaction diagram
elimination reaction
-
-
?
L-serine-O-sulfate
? + NH3
show the reaction diagram
-
elimination reaction
-
-
?
L-serine-O-sulfate
O-sulfopyruvate + NH3
show the reaction diagram
-
elimination reaction
-
-
?
L-Thr
3-Hydroxy-2-oxobutyrate + NH3
show the reaction diagram
L-threo-3-hydroxyaspartate
oxaloacetate + NH3
show the reaction diagram
-
-
-
?
L-threonine
2-oxo-butanoate + NH3
show the reaction diagram
-
-
-
?
L-threonine
2-oxobutyrate + NH3
show the reaction diagram
L-threonine
3-hydroxy-2-butenoic acid + NH3
show the reaction diagram
-
alpha,beta-elimination reaction
-
-
?
L-threonine
alpha-ketobutyrate + NH3
show the reaction diagram
L-Trp
?
show the reaction diagram
additional information
?
-
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-Ser
?
show the reaction diagram
L-serine
pyruvate + NH3
show the reaction diagram
L-threonine
alpha-ketobutyrate + NH3
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
additional information
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
-
nonspecific requirement for a monovalent or bivalent cation. Half-maximal activity is produced with 22.5 mM KCl
NH4+
-
slight stimulation
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
2-oxobutyrate
20 mM: 49.3% inhibition, not reversed by 5 mM AMP
AlK(SO4)2
-
-
ammonia
product inhibition, noncompetitive
Cu2+
-
inhibition of both activities
CuCl2
-
0.7 mM, 50% inhibition
D-serine
ethanolamine
Fe2+
-
slight inhibition of both activities
glyoxylate
20 mM: 54.1% inhibition, not reversed by 5 mM AMP
homocysteine
-
noncompetitive with respect to substrate, competitive with regard to pyridoxal 5'-phosphate
hydroxylamine
-
-
imidazole
-
-
L-alanine
-
-
L-cysteine
L-Thr
-
competitive
L-threonine
-
100 mM, 56% inhibition
NH4Cl
-
significant fall in the serine-dehydratase expression during experimental chronic acidosis, acidosis is induced by ingestion of 0.28 M ammonium chloride solution
oxygen
pyruvate
Zn2+
-
inhibition of both activities
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
leucine
excess leucine intake strongly induces SDH activity in the liver but not in the kidney
sulfhydryl reagents
Clostridium acidi-urici
-
required
additional information
-
the enzyme is inactive in crude extract and can be activated with iron and dithiothreitol. The activation requires oxygen, and is inhibited by free radical scavengers and by diethylenentriamine pentaacetic acid, which prevents Fe cycling
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.2 - 75
D-serine
55 - 60
D-threonine
0.8 - 420
L-Ser
0.00258 - 182
L-serine
0.49
L-serine O-sulfate
-
pH 8.0, 37C, presence of 1 mM ATP, elimination reaction
130
L-Thr
-
in presence and in absence of 20 mM NH4Cl
0.5 - 57
L-threonine
30.7 - 67.3
serine
3.1 - 59.5
threonine
additional information
additional information
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.6
beta-chloro-L-alanine
Mus musculus
-
pH 8.0, 37C, presence of 1 mM ATP, elimination reaction
0.0033 - 14.5
D-serine
0.028 - 0.3
D-threonine
323 - 512
L-Ser
0.033 - 585
L-serine
0.49
L-serine O-sulfate
Mus musculus
-
pH 8.0, 37C, presence of 1 mM ATP, elimination reaction
31
L-threo-3-hydroxyaspartate
Mus musculus
-
pH 8.0, 37C, presence of 1 mM ATP, elimination reaction
5.2 - 10.5
L-threonine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
18 - 230
L-Ser
0.2 - 57
L-serine
0.7
L-threonine
Entamoeba histolytica
B1N2N4
-
250
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.7
CuCl2
-
-
1.41 - 10
D-serine
0.9
L-alanine
-
pH 8.0, 37C
0.1 - 2.2
L-cysteine
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
10
ATP
Entamoeba histolytica
B1N2N4
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0006
kidney, diet 10% casein; kidney, diet Leu
0.0008
kidney, diet 20% casein; kidney, diet Ile; kidney, diet Val
0.01775
-
effect of chronic acidosis
0.034
liver, diet Ile
0.0365
liver, diet 10% casein
0.041
-
strain DL-1
0.0416
liver, diet Val
0.04264
-
control
0.1262
liver, diet 20% casein
0.1419
liver, diet Leu
96
-
substrate L-threonine, pH 8.3, 37C
115
-
recombinant SdaA
116
-
substrate L-threonine, pH 8.3, 37C
137
-
substrate L-serine, pH 8.3, 37C
174.2
-
isoenzyme II
200
-
substrate L-serine, pH 8.3, 37C
226.9
-
isoenzyme I
307
-
anaerobically isolated enzyme, pH 8.0
additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 10
6.5 - 9.5
-
pH 6.5: about 40% of maximal activity, pH 9.5: about 90% of maximal activity
6.5
-
negligible activity below
7 - 9.5
-
pH 7: about 35% of maximal activity, pH 9.5: about 35% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
activity assay
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
18 - 50
-
18C: about 50% of maximal activity, 50C: about 25% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
cancer cell line-specific isozyme cSDH
Manually annotated by BRENDA team
-
hepatic SDH
Manually annotated by BRENDA team
-
cancerous SDH
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Staphylococcus aureus (strain Newman)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30500
-
gel filtration
34100
-
determined by SDS-PAGE and immunoblot
34630
-
hSDH, calculated molecular weight
34670
-
cSDH, calculated molecular weight
35000 - 40000
-
gel filtration
35680
His-tagged fusion protein, calculated from cDNA
49480
-
gel filtration, monomer
53000
-
gel filtration
55000
-
isoforms A and B, gel filtration
64000
-
ultracentrifugation
66810
-
laser light scattering
68000
-
sucrose density gradient centrifugation
72000
Clostridium acidi-urici
-
gel filtration
78000
-
gel filtration
98950
-
gel filtration, dimer
101700
-
dynamic light scattering
107000
-
gel filtration
123000
-
gel filtration
130000
-
gel filtration
150000
-
gel filtration
180000
-
gradient PAGE
200000
-
gel filtration
230000
-
gel filtration in absence of Fe2+, octameric enzyme form
250000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
-
3 * 25000 + 3 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers
monomer
octamer
tetramer
additional information
structure analysis and comparison to the rat and the human liver isozymes, the cancer cell isozyme and the liver isozyme show different active site surface amino acid residues, overview
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure obtained by molecular replacement shows a homodimer and a fold typical for beta-family pyridoxal 5'-phosphate-dependent enzymes. Each monomer serves as an active unit
-
hanging-drop vapour diffusion, 0.002 ml protein solution containing 20-30 mg/ml SDH in 20 mM Tris-HCl, pH 7.6 and 150 mM NaCl is mixed with 0.002 ml reservoir solution containing 800 mM ammonium sulfate in 100 mM Tris-HCl, pH 7.0-8.0, crystals diffract to 2.5 A
-
purified recombinant cSDH, hanging drop vapour diffusion method, 10 mg/ml protien in 50 mM Na-citrate, pH 5.6, 10 mM DL-O-methylserine, 200 mM potassium acetate, 5 mM dithiothreitol, 15% w/v PEG-8000 at 21C, 1 week, X-ray diffraction structure determination and analysis at 2.8 A resolution
structure of A65S hSDH mutant is determined at 1.3 A resolution
-
crystal structures of apo-SDH and holo-SDH, crystallized with O-methylserine, at 2.8 A and 2.6 A resolution, respectively
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
37C, 30 min, about 50% loss of activity
210781
5.5
-
37C, 30 min, about 40% loss of activity
210781
6 - 7
-
37C, 30 min, about 25% loss of activity
210781
8
-
37C, 30 min, about 45% loss of activity
210781
8.5
-
37C, 30 min, 50% loss of activity
210781
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0
-
30 min, 45% loss of activity
30
-
pH 6.2, 30 min, stable up to
37
-
complete loss of activity within 30 min. Fe2+, L-Ser D-Ser or ethanolamine decrease the loss of activity at 37C
40
-
pH 6.2, 30 min, about 50% loss of activity
60
-
10 min, about 75% loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
extreme instability does not permit purification to homogeneity
-
it is absolutely critical that dilutions of the purified enzyme be made in buffer containing 50% glycerol, otherwise the enzyme rapidly loses activity
-
L-Cys and D-Ser stabilize enzyme activity
-
suszeptible to proteases e.g. trypsin
-
unstable in all attempts at purification
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
complete loss of activity in crude extracts after exposure to air for 1 h
-
650851
inactivated upon exposure to air, reactivated by Fe2+ under aerobic conditions
purified SdaA is inactivated with a half-life of approx. 1.5 h upon exposure to air, inactivated SdaA can be reactivated to approx. 60% of its activity under strict anaerobic conditiones with Fe2+ and dithiothreitol
-
651494
rapid loss of activity upon exposure to air, reactivation by Fe2+
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-10C, 40% glycerol, loss of activity within 1 week
-
-20C, 40% loss of activity after 24 h, 0.76 mg/ml protein concentration, partially purified enzyme
-
-20C, pH 7.0-8.0, stable over many months, enzyme in crude extract
-
-70C, 0.6 mg/ml protein, 30% loss of activity after 1 month, purified enzyme
-
-80C, at least 1 month, no loss of activity
-
-80C, stable for more than 2 weeks
-
0C, 45% loss of activity after 30 min
-
0C, stable for at least 2 weeks
-
4C, 90% loss of activity after 24 h, 0.76 mg/ml protein concentration, partially purified enzyme
-
unstable within the cell in the presence of its inducers, Gly and Leu, but not in their absence
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
anaerobic purification of His-tagged enzyme, purified protein is brown in colour
-
both isoforms A and B
-
cSDH is purified using a Sephacryl S-200 and a Ni2+-NAT column
-
expression in Escherichia coli with N-terminal His-tag, purification protocol from inclusion bodies
-
immobilized metal ion affinity chromatography (Ni2+)
partial
partially purified
-
proteins of crude extracts are fractionated using a DEAE-Sephadex A-25 column
recombinant cancer cell isozyme cSDH to homogeneity by ammonium sulfate fractionation, dialysis, anion exchange and nickel affinity chromatography
recombinant enzyme expressed in insect cells
-
recombinant His-tagged SdaA
-
recombinant protein expressed in Escherichia coli
recombinant protein, purification under anaerobic conditions
-
recombinant SDH
use of gene fusion of the structural gene sdaA to purify L-serine deaminase 1
-
using cobalt-based affinity columns
using cobalt-based Talon immobilized metal affinity columns
-
using Ni-NTA chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cancer cell isozyme cSDH, expression in Escherichia coli strain BL21
expressed in Escherichia coli as a His-tagged fusion protein
expression in Escherichia coli
gene tcdB, phylogenetic analysis of threonine ammonia-lyases
-
His-tagged version expressed in Escherichia coli BL21(DE3)
the cSDH sequence is cloned into the pCW and pET28a vector for expression of the protein in Escherichia coli BL21DE3 cells
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A65G
site-directed mutagenesis of the human liver isozyme cSDH, large structural alterations, serine binding is not affected, overview
A65S
-
structure of A65S hSDH mutant is determined at 1.3 A resolution. Mutant shows decreased activity (50%) with substrate L-serine compared to wild-type. Mutant shows measurable activity with substrate D-serine
A65S/V225S
-
double mutant shows only 10% of activity with substrate L-serine compared to wild-type (100%). Double mutant shows very little but measurable activity with substrate D-serine
C303A
site-directed mutagenesis of the human liver isozyme cSDH, structural alterations, overview
C309A
site-directed mutagenesis of the cancer cell isozyme cSDH, structural alterations, overview
cSDH-hSDH
-
chimeric protein
DELTAP128
-
hSDH
G72A
site-directed mutagenesis of the cancer cell isozyme cSDH, large structural alterations, serine binding is not affected, changing alanine to glycine at residue 72 in cSDH is responsible for the reduced catalytic activity of cSDH, overview
G72A/S228A
site-directed mutagenesis of the cancer cell isozyme cSDH, catalytic activities for both the substrates are substantially recovered, overview
InsP128
-
cSDH, cSDH lacks a Pro residue corresponding to Pro128 in hSDH
L287V
-
cSDH
C183A
135% of wild-type activity. Enzyme retains the positive cooperativity seen in the native enzyme
C221A
70% of wild-type activity. Enzyme retains the positive cooperativity seen in the native enzyme
C226A
100% of wild-type activity. Enzyme retains the positive cooperativity seen in the native enzyme
C304A
10% of wild-type activity. Mutant displays altered kinetics with a higher Km and a Hill coefficient indicating negative homotropic cooperativity
C343A
inactive, mutants lacks the charge transfer absorbance at 400 nm that is indicative of the 4Fe-4S center
C385A
inactive, mutants lacks the charge transfer absorbance at 400 nm that is indicative of the 4Fe-4S center
C396A
inactive, mutants lacks the charge transfer absorbance at 400 nm that is indicative of the 4Fe-4S center
C458A
44% of wild-type activity. Enzyme retains the positive cooperativity seen in the native enzyme
H152S
-
ratio of elimination reaction to racemization is 1.4 compared to 3.7 in wild-type
N154F
-
ratio of elimination reaction to racemization is 0.33 compared to 3.7 in wild-type
P153S
-
ratio of elimination reaction to racemization is 0.24 compared to 3.7 in wild-type
Q155D
-
ratio of elimination reaction to racemization is 0.25 compared to 3.7 in wild-type
additional information
-
construction of a mutant strain devoid of functional genes sdaA, sdaB, tdcG encoding the three isozymes of the organism, the loss of the ability to deaminate L-serine severely impairs growth and cell division in Escherichia coli K-12 leading e.g. to filamentation, phenotype, overview
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
medicine
-
loss of serine deaminase activity results in a hypercolonization phenotype, hypercolonization plays a role in urinary tract infections
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