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Enzyme Nomenclature
Information on EC 4.3.1.17 - L-serine ammonia-lyase
for references in articles please use BRENDA:EC4.3.1.17
Word Map on EC 4.3.1.17
- 4.3.1.17
- pyridoxal
-
deamination
- glucagon
-
gluconeogenesis
-
gluconeogenic
-
carboxykinase
-
hydroxymethyltransferase
- d-serine
- l-isoleucine
-
peptostreptococcus
-
plp-dependent
- 2-oxobutyrate
- asaccharolyticus
- deaminases
- analysis
- medicine
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
4.3.1.17
-
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RECOMMENDED NAME
GeneOntology No.
L-serine ammonia-lyase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-aminoprop-2-enoate = 2-iminopropanoate
(1b), spontaneous
-
-
-
2-iminopropanoate + H2O = pyruvate + NH3
(1c), spontaneous
-
-
-
L-serine = 2-aminoprop-2-enoate + H2O
(1a)
-
-
-
L-serine = pyruvate + NH3
A pyridoxal-phosphate protein.; A pyridoxal-phosphate protein. This reaction is also carried out by EC 4.3.1.19 threonine ammonia-lyase, from a number of sources. The reaction catalysed probably involves initial elimination of water, hence the enzyme's original classification as EC 4.2.1.13, L-serine dehydratase, followed by isomerization and hydrolysis of the product with C-N bond breakage; (overall reaction)
-
-
-
L-serine = pyruvate + NH3
reaction analysis by ab initio quantum mechanical/molecular mechanical method, the reaction involves a Schiff base formation step and a proton-relaying mechanism involving the phosphate of the cofactor in the beta-hydroxyl-leaving step following sequentially after the elimination of the alpha-proton, leading to a single but sequential alpha,beta-elimination step. The rate-limiting transition state is specifically stabilized by the enzyme environment, catalytic mechanism involving Lys41 in the active site, detailed overview
-
L-serine = pyruvate + NH3
pre-steady-state kinetic analysis of L-serine binding to lpLSD demonstrates that L-serine binds to a second noncatalytic site and produces a conformational change in the enzyme. The rate of this conformational change is too slow for its participation in the catalytic cycle but rather occurs prior to catalysis to produce an activated form of the enzyme
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
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
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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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.
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CAS REGISTRY NUMBER
COMMENTARY
9014-27-1
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
bifunctional enzyme, racemization of serine and elimination of L-serine and L-serine-O-sulfate to form pyruvate
-
-
bifunctional enzyme, racemization of serine and elimination of L-serine and L-serine-O-sulfate to form pyruvate
Swissprot
bifunctional enzymes, racemization of serine and alpha,beta-elimination of L-serine
-
-
isoforms A and B, bifunctional enzymes, racemization of serine and elimination of L-serine and L-serine-O-sulfate to form pyruvate
-
-
-
-
-
SDH activity and its gene expression are induced in both growing and mature rats when their protein intake exceeds their nutrintional requirements
-
-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
Escherichia coli K-12 provided with glucose and a mixture of amino acids depletes L-serine more quickly than any other amino acid even in the presence of ammonium sulfate. A mutant lacking 4Fe4S L-serine deaminases SdaA, SdaB, and TdcG is unable to do this. The high level of L-serine that accumulates when the mutant is exposed to amino acid mixtures starves the cells for C1 units and interferes with cell wall synthesis. Growth in minimal medium containing glucose, ammonium sulfate, and Casamino Acids results in deformed cells and frequently lysing, which can be reversed by adding S-adenosylmethionine; Escherichia coli K-12 provided with glucose and a mixture of amino acids depletes L-serine more quickly than any other amino acid even in the presence of ammonium sulfate. A mutant lacking 4Fe4S L-serine deaminases SdaA, SdaB, and TdcG is unable to do this. The high level of L-serine that accumulates when the mutant is exposed to amino acid mixtures starves the cells for C1 units and interferes with cell wall synthesis. Growth in minimal medium containing glucose, ammonium sulfate, and Casamino Acids results in deformed cells and frequently lysing, which can be reversed by adding S-adenosylmethionine; Escherichia coli K-12 provided with glucose and a mixture of amino acids depletes L-serine more quickly than any other amino acid even in the presence of ammonium sulfate. A mutant lacking 4Fe4S L-serine deaminases SdaA, SdaB, and TdcG is unable to do this. The high level of L-serine that accumulates when the mutant is exposed to amino acid mixtures starves the cells for C1 units and interferes with cell wall synthesis. Growth in minimal medium containing glucose, ammonium sulfate, and Casamino Acids results in deformed cells and frequently lysing, which can be reversed by adding S-adenosylmethionine
physiological function
cytotoxic early protein 77 of mycobacteriophage L5 interacts with MSMEG_3532
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-allo-threonine
2-oxobutyrate + NH3
-
at 4.6% of the rate with L-serine
-
-
?
L-threonine
3-hydroxy-2-butenoic acid + NH3
-
alpha,beta-elimination reaction
-
-
?
L-Leu
3-Hydroxy-2-oxopropionate + NH3
-
3% of the activity with L-Ser
-
-
-
L-Leu
3-Hydroxy-2-oxopropionate + NH3
-
3% of the activity with L-Ser
-
-
-
L-serine
pyruvate + NH3
-
specific for L-Ser
-
-
L-serine
pyruvate + NH3
SDH is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes dehydration of L-Ser/Thr to yield pyruvate/ketobutyrate and ammonia
-
-
?
L-serine
pyruvate + NH3
a rigid pyridine ring pocket is necessary for cSDH having a flexible substrate binding-loop
-
-
?
L-serine
pyruvate + NH3
-
wild-type enzyme shows almost no activity with D-serine
-
-
?
L-Thr
2-oxobutanoate + NH3
-
1% of the activity with L-Ser
-
-
-
L-Thr
2-oxobutanoate + NH3
-
1% of the activity with L-Ser
-
-
-
L-Thr
2-oxobutanoate + NH3
Q5ZXE1
Km -value is approximately 150 times that for L-serine. At an L-threonine concentration of 300 mM, the enzyme activity is approximately 5% of the activity for L-serine at its Km of 2 mM
-
-
?
additional information
?
-
-
no substrate: D-serine. Extremely poor substrate: L-cysteine
-
-
-
additional information
?
-
-
GSU0486 mainly catalyzes the deamination of L-threonine, EC 4.3.1.19
-
-
-
additional information
?
-
Geobacter sulfurreducens ATCC 51573 / DSM 12127
-
GSU0486 mainly catalyzes the deamination of L-threonine, EC 4.3.1.19
-
-
-
additional information
?
-
-
GSU0486 mainly catalyzes the deamination of L-threonine, EC 4.3.1.19
-
-
-
additional information
?
-
-
enzyme shows homotopic cooperativity, Hill coefficient of wild-type is 1.7
-
-
-
additional information
?
-
Q5ZXE1
enzyme shows homotopic cooperativity, Hill coefficient of wild-type is 1.7
-
-
-
additional information
?
-
racemization and elimination activities reside at the same active site of enzyme. Racemization activity is specific to serine, elimination activity has a broader specificity for L-amino acids with a suitable leaving group at the beta-carbon
-
-
-
additional information
?
-
-
ration of elimination reaction/racemization reaction for substrate L-serine is 3.7
-
-
-
additional information
?
-
cytotoxic early protein 77 of mycobacteriophage L5 interacts with MSMEG_3532
-
-
-
additional information
?
-
the enzyme does not show 1-aminocyclopropane-1-carboxylate deaminase activity at high temperature as well as at room temperature though it has significant sequence similarity to 1-aminocyclopropane-1-carboxylate deaminase from the yeast Hansenula saturnus
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
A0QY48
cytotoxic early protein 77 of mycobacteriophage L5 interacts with MSMEG_3532
-
-
-
L-serine
pyruvate + NH3
Q96GA7
SDH is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes dehydration of L-Ser/Thr to yield pyruvate/ketobutyrate and ammonia
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
-
Km: 0.0003 mM; one mol of enzyme contains two mol of pyridoxal phosphate
pyridoxal 5'-phosphate
-
coenzyme; K+ and NH4+ decrease the dissociation constant of pyridoxal 5'-phosphate. Tris and the substrate compete for pyridoxal 5'-phosphate with the enzyme because of Schiff's base formation. Influence of substrate concentration on the Km-value of pyridoxal 5'-phosphate
pyridoxal 5'-phosphate
-
prosthetic group; pyridoxal-5'-phosphate-independent enzyme
pyridoxal 5'-phosphate
-
pyridoxal-5'-phosphate-independent enzyme
pyridoxal 5'-phosphate
-
pyridoxal-5'-phosphate-independent enzyme
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate is sandwiched between F40 and A222
pyridoxal 5'-phosphate
SDH is a pyridoxal 5'-phosphate-dependent enzyme, PLP is covalently attached to K48 by Schiff-base linkage in the active site. The ring nitrogen of PLP is involved in a H-bonding with C309, but is apparently not protonated
pyridoxal 5'-phosphate
cofactor is located in the crevice between the two domains, attached to residue Lys52 by a Schiff-base linkage
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Fe2+
Iron
K+
KCl
-
nonspecific requirement for a monovalent or bivalent cation. Half-maximal activity is produced with 22.5 mM KCl
Mg2+
MgCl2
Mn2+
Iron
-
7.7 mol iron per mol dimer, two (4Fe-4S)2+ clusters per dimer in anaerobically isolated enzyme, exposure to air results in loss of clusters and concomitant loss of enzyme activity
Iron
-
presence of (4Fe-4S)2+ and of (2Fe-2S)2+ clusters involved in catalytic turnover
Iron
-
enzyme probably contains a diamagnetic [4Fe-4S]2+cluster which is converted by oxidation and loss of iron ion to a paramegnetic [3Fe-4S]+cluster resulting in inactivation of the enzyme
Iron
-
the enzyme contains 3.8 mol Fe and 5.6 mol inorganic sulfur per mol of heterodimer, indicating the presence of an [Fe-S]center
MgCl2
-
nonspecific requirement for a monovalent or bivalent cation. Half-maximal activity with 1.0 mM MgCl2
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
homocysteine
-
noncompetitive with respect to substrate, competitive with regard to pyridoxal 5'-phosphate
NH4Cl
-
significant fall in the serine-dehydratase expression during experimental chronic acidosis, acidosis is induced by ingestion of 0.28 M ammonium chloride solution
ATP
-
inhibitory to L-serine O-sulfate dehydration reaction, activating for racemization reraction
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
leucine
excess leucine intake strongly induces SDH activity in the liver but not in the kidney
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
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.49
L-serine O-sulfate
-
pH 8.0, 37°C, presence of 1 mM ATP, elimination reaction
12
D-serine
-
mutant Q155D, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
55
D-threonine
-
wild-type, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
60
D-threonine
-
mutant Q155D, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
2
L-Ser
Q5ZXE1
wild-type, pH 7.0, temperature not specified in the publication
2.2
L-Ser
Q5ZXE1
mutant C183A, pH 7.0, temperature not specified in the publication
2.7
L-Ser
Q5ZXE1
mutant C226A, pH 7.0, temperature not specified in the publication
3
L-Ser
Q5ZXE1
mutant C221A, pH 7.0, temperature not specified in the publication
6.9
L-Ser
Q5ZXE1
mutant C458A, pH 7.0, temperature not specified in the publication
17.8
L-Ser
Q5ZXE1
mutant C304A, pH 7.0, temperature not specified in the publication
0.00258
L-serine
pH 7, temperature not specified in the publication, Vmax: 11.7/min/mg
5.1
L-serine
Q5ZXE1
pH 7, temperature not specified in the publication
11
L-serine
-
mutant Q155D, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
13.6
L-serine
-
pH 7, temperature not specified in the publication, 100 mM KCl
25.5
L-serine
-
pH 7, temperature not specified in the publication, 300 mM KCl
29.2
L-serine
-
pH 7, temperature not specified in the publication, 500 mM KCl
182
L-serine
-
pH 7.4, 25°C, animals treated with thioacetamide for 97 days
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.6
beta-chloro-L-alanine
-
pH 8.0, 37°C, presence of 1 mM ATP, elimination reaction
0.49
L-serine O-sulfate
-
pH 8.0, 37°C, presence of 1 mM ATP, elimination reaction
31
L-threo-3-hydroxyaspartate
-
pH 8.0, 37°C, presence of 1 mM ATP, elimination reaction
0.012
D-serine
-
mutant Q155D, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
0.042
D-serine
-
wild-type, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
0.028
D-threonine
-
mutant Q155D, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
0.3
D-threonine
-
wild-type, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
323
L-Ser
Q5ZXE1
mutant C304A, pH 7.0, temperature not specified in the publication
330
L-Ser
Q5ZXE1
wild-type, pH 7.0, temperature not specified in the publication
359
L-Ser
Q5ZXE1
mutant C221A, pH 7.0, temperature not specified in the publication
467
L-Ser
Q5ZXE1
mutant C226A, pH 7.0, temperature not specified in the publication
506
L-Ser
Q5ZXE1
mutant C183A, pH 7.0, temperature not specified in the publication
512
L-Ser
Q5ZXE1
mutant C458A, pH 7.0, temperature not specified in the publication
0.033
L-serine
-
mutant Q155D, presence of ATP, pH 7.4, 37°C; wild-type, alpha,beta-elimination, pH 7.4, 37°C
0.166
L-serine
-
wild-type, alpha,beta-elimination, presence of ATP, pH 7.4, 37°C
184
L-serine
-
pH 7, temperature not specified in the publication, 100 mM KCl
286
L-serine
Q5ZXE1
pH 7, temperature not specified in the publication
465
L-serine
-
pH 7, temperature not specified in the publication, 300 mM KCl
585
L-serine
-
pH 7, temperature not specified in the publication, 500 mM KCl
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
18
L-Ser
Q5ZXE1
mutant C304A, pH 7.0, temperature not specified in the publication
74
L-Ser
Q5ZXE1
mutant C458A, pH 7.0, temperature not specified in the publication
120
L-Ser
Q5ZXE1
mutant C221A, pH 7.0, temperature not specified in the publication
170
L-Ser
Q5ZXE1
mutant C226A, pH 7.0, temperature not specified in the publication; wild-type, pH 7.0, temperature not specified in the publication
230
L-Ser
Q5ZXE1
mutant C183A, pH 7.0, temperature not specified in the publication
14
L-serine
-
pH 7, temperature not specified in the publication, 100 mM KCl
18
L-serine
-
pH 7, temperature not specified in the publication, 300 mM KCl
20
L-serine
-
pH 7, temperature not specified in the publication, 500 mM KCl
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
10
D-serine
Q5ZXE1
pH 7.0, temperature not specified in the publication
0.1
L-cysteine
Q5ZXE1
pH 7.0, temperature not specified in the publication
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.3
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 10
6.5 - 9.5
-
pH 6.5: about 40% of maximal activity, pH 9.5: about 90% of maximal activity
7 - 9.5
-
pH 7: about 35% of maximal activity, pH 9.5: about 35% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
40
50
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
18 - 50
-
18°C: about 50% of maximal activity, 50°C: about 25% of maximal activity
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
enzyme activity increases with age of animals and also in response to the amount of surplus amino acids from dietary protein. Induction is mainly controlled at the level of transcription and seems not to be related to gluconeogenesis
-
suffering chronic injury caused by ingestion of thioacetamide. After 97 days of intake, enzyme activity is about 60% lower than in controls. No significant differences in Km-value are found, while enzyme protein level is reduced. Enzyme is localized to periportal zone of the hepatic acinus
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
Q5ZXE1
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10000
-
1 * 26000 + 1 * 10000, enzyme either exists as a heterooctamer or a heterodimer, SDS-PAGE
25000
-
1 * 25000 + 1 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers; 2 * 25000 + 2 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers; 3 * 25000 + 3 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers; 4 * 25000 + 4 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers
26000
-
1 * 26000 + 1 * 10000, enzyme either exists as a heterooctamer or a heterodimer, SDS-PAGE; 4 * 26000 + 4 * 30000, enzyme either exists as a heterooctamer or a heterodimer, SDS-PAGE
30000
34000
40000
46000
-
2 * 52910, calculated for His-tagged protein, 2 * 48460, calculated for native protein, 2 * 46000, SDS-PAGE of His-tagged protein
48460
-
2 * 52910, calculated for His-tagged protein, 2 * 48460, calculated for native protein, 2 * 46000, SDS-PAGE of His-tagged protein
49476
-
gel filtration, 1 * 49476, monomeric form does not possess enzymatic activity; gel filtration, 2 * 49476, only dimer displays catalytic activity. In the absence of substrate, lpLSD is predominately a dimer
52910
-
2 * 52910, calculated for His-tagged protein, 2 * 48460, calculated for native protein, 2 * 46000, SDS-PAGE of His-tagged protein
57000
60000
30000
-
1 * 25000 + 1 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers; 2 * 25000 + 2 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers; 3 * 25000 + 3 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers; 4 * 25000 + 4 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers
30000
-
4 * 26000 + 4 * 30000, enzyme either exists as a heterooctamer or a heterodimer, SDS-PAGE
57000
-
gel filtration in presence of 10 mM Fe2+, dimeric enzyme form
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
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
dimer
-
1 * 26000 + 1 * 10000, enzyme either exists as a heterooctamer or a heterodimer, SDS-PAGE
dimer
-
2 * 52910, calculated for His-tagged protein, 2 * 48460, calculated for native protein, 2 * 46000, SDS-PAGE of His-tagged protein
dimer
-
gel filtration, 2 * 49476, only dimer displays catalytic activity. In the absence of substrate, lpLSD is predominately a dimer
dimer
-
1 * 25000 + 1 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers
monomer
-
gel filtration, 1 * 49476, monomeric form does not possess enzymatic activity
octamer
-
4 * 26000 + 4 * 30000, enzyme either exists as a heterooctamer or a heterodimer, SDS-PAGE
octamer
-
4 * 25000 + 4 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers
tetramer
-
2 * 25000 + 2 * 30000, the enzyme is composed of two different subunits in a 1:1 stoichiometry, forming heterodimers to heterooctamers
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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 21°C, 1 week, X-ray diffraction structure determination and analysis at 2.8 A resolution
hanging-drop vapor-diffusion method, crystal structures of the native and 1-aminocyclopropane-1-carboxylate-complexed enzyme. The crystals of native and Se-Met belong to the space group P3(2)21 with unit cell parameters of a=b= 122.3 A, c = 115.0 A, and gamma = 120°, and there are three molecules in an asymmetric unit. The crystals of the ACC complex belong to space group P1 with unit cell parameters of a = 105.8 A, b = 147.2 A, c = 149.0 A, a = 73.18, b = 90.18, and gamma = 68.48, and 24 molecules are included in an asymmetric cell
crystal structures of apo-SDH and holo-SDH, crystallized with O-methylserine, at 2.8 A and 2.6 A resolution, respectively
-
to 1.76 A resolution. The active site is located between the small domain and large domain, and a pyridoxal 5'-phosphate is attached to Lys52 by a Schiff-base linkage
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
-
complete loss of activity within 30 min. Fe2+, L-Ser D-Ser or ethanolamine decrease the loss of activity at 37°C
40
45
50
55
55
-
complete loss of activity after 4 min. NH4Cl, KCl or (NH4)2SO4 stabilize
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
it is absolutely critical that dilutions of the purified enzyme be made in buffer containing 50% glycerol, otherwise the enzyme rapidly loses activity
-
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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+
inactivated upon exposure to air, reactivated by Fe2+ under aerobic conditions
-
210790
inactivated upon exposure to air, reactivated by Fe2+ under aerobic conditions
-
210791
rapid loss of activity upon exposure to air, reactivation by Fe2+
-
210794
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 40% loss of activity after 24 h, 0.76 mg/ml protein concentration, partially purified enzyme
-
-20°C, pH 7.0-8.0, stable over many months, enzyme in crude extract
-
-70°C, 0.6 mg/ml protein, 30% loss of activity after 1 month, purified enzyme
-
4°C, 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
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
anaerobic purification of His-tagged enzyme, purified protein is brown in colour
-
expression in Escherichia coli with N-terminal His-tag, purification protocol from inclusion bodies
-
partial
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 protein expressed in Escherichia coli
recombinant SDH
use of gene fusion of the structural gene sdaA to purify L-serine deaminase 1
-
using cobalt-based affinity columns
using Ni-NTA chromatography
proteins of crude extracts are fractionated using a DEAE-Sephadex A-25 column
-
proteins of crude extracts are fractionated using a DEAE-Sephadex A-25 column
-
proteins of crude extracts are fractionated using a DEAE-Sephadex A-25 column
-
proteins of crude extracts are fractionated using a DEAE-Sephadex A-25 column
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli as a His-tagged fusion protein
expression in Escherichia coli
the cSDH sequence is cloned into the pCW and pET28a vector for expression of the protein in Escherichia coli BL21DE3 cells
-
expressed in Escherichia coli as a His-tagged fusion protein
-
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
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
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
C183A
Q5ZXE1
135% of wild-type activity. Enzyme retains the positive cooperativity seen in the native enzyme
C221A
Q5ZXE1
70% of wild-type activity. Enzyme retains the positive cooperativity seen in the native enzyme
C226A
Q5ZXE1
100% of wild-type activity. Enzyme retains the positive cooperativity seen in the native enzyme
C304A
Q5ZXE1
10% of wild-type activity. Mutant displays altered kinetics with a higher Km and a Hill coefficient indicating negative homotropic cooperativity
C343A
Q5ZXE1
inactive, mutants lacks the charge transfer absorbance at 400 nm that is indicative of the 4Fe-4S center
C385A
Q5ZXE1
inactive, mutants lacks the charge transfer absorbance at 400 nm that is indicative of the 4Fe-4S center
C396A
Q5ZXE1
inactive, mutants lacks the charge transfer absorbance at 400 nm that is indicative of the 4Fe-4S center
C458A
Q5ZXE1
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
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
medicine
-
loss of serine deaminase activity results in a hypercolonization phenotype, hypercolonization plays a role in urinary tract infections
analysis
-
online-determination of L-serine concentation in bioreactor
analysis
Q5ZXE1
development of a simple, direct, and continuous assay based on the absorbance of pyruvate, the product of the dehydratase reaction
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LINKS TO OTHER DATABASES (specific for EC-Number 4.3.1.17)
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