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Information on EC 4.3.1.17 - L-serine ammonia-lyase and Organism(s) Rattus norvegicus and UniProt Accession P09367

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EC Tree
     4 Lyases
         4.3 Carbon-nitrogen lyases
             4.3.1 Ammonia-lyases
                4.3.1.17 L-serine ammonia-lyase
IUBMB Comments
Most enzymes that catalyse this reaction are pyridoxal-phosphate-dependent, although some enzymes contain an iron-sulfur cluster instead . 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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This record set is specific for:
Rattus norvegicus
UNIPROT: P09367
Word Map
The taxonomic range for the selected organisms is: Rattus norvegicus
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
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Synonyms
serine dehydratase, l-serine dehydratase, l-threonine deaminase, l-threonine dehydratase, l-serine deaminase, serine deaminase, serdh, lplsd, l-sd2, msmeg_3532, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Dehydratase, L-serine
-
-
-
0
L-Hydroxy amino acid dehydratase
-
-
-
0
L-SD
-
-
-
0
L-SD1
-
-
-
0
L-SD2
-
-
-
0
L-serine ammonia-lyase
L-Serine deaminase
-
-
-
0
L-serine dehydratase
283085
-
SD
-
-
-
0
Serine deaminase
-
-
-
0
Serine dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-serine = pyruvate + NH3
show the reaction diagram
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
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
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
L-serine
pyruvate + NH3
show the reaction diagram
L-serine
pyruvate + NH3
show the reaction diagram
L-Thr
2-oxobutanoate + NH3
show the reaction diagram
-
-
-
-
?
L-threonine
2-oxo-butanoate + NH3
show the reaction diagram
-
-
-
?
L-threonine
2-oxobutyrate + NH3
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-serine
pyruvate + NH3
show the reaction diagram
L-serine
pyruvate + NH3
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
pyridoxal 5'-phosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
slight stimulation
NH4+
-
slight stimulation
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
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
PCMB
-
NH4+ protects
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
leucine
excess leucine intake strongly induces SDH activity in the liver but not in the kidney
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
70 - 100
L-Ser
45 - 182
L-serine
130
L-Thr
-
in presence and in absence of 20 mM NH4Cl
50 - 57
L-threonine
additional information
additional information
-
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0006
0.0008
0.034
liver, diet Ile
0.0365
liver, diet 10% casein
0.0416
liver, diet Val
0.1262
liver, diet 20% casein
0.1419
liver, diet Leu
0.01775
-
effect of chronic acidosis
0.04264
-
control
116
-
substrate L-threonine, pH 8.3, 37°C
174.2
-
isoenzyme II
200
-
substrate L-serine, pH 8.3, 37°C
226.9
-
isoenzyme I
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
-
activity assay
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
activity assay
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
SDHL_RAT
363
0
38433
Swiss-Prot
other Location (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
34000
34100
-
determined by SDS-PAGE and immunoblot
35000
-
2 * 35000, SDS-PAGE
35000 - 40000
-
gel filtration
60000
-
gel filtration
64000
-
ultracentrifugation
66000
66810
-
laser light scattering
68000
-
sucrose density gradient centrifugation
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structures of apo-SDH and holo-SDH, crystallized with O-methylserine, at 2.8 A and 2.6 A resolution, respectively
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55
-
complete loss of activity after 4 min. NH4Cl, KCl or (NH4)2SO4 stabilize
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
suszeptible to proteases e.g. trypsin
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, at least 1 month, no loss of activity
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant protein expressed in Escherichia coli
-
recombinant SDH
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yeung, Y.G.; Yeung, D.
Comparative studies on threonine and serine dehydratases in rat liver
Int. J. Biochem.
11
161-164
1980
Rattus norvegicus
Manually annotated by BRENDA team
Grillo, M.A.
Serine dehydratase in animal tissues
Acta Vitaminol. Enzymol.
27
51-61
1973
Gallus gallus, Rattus norvegicus
Manually annotated by BRENDA team
Simon, D.; Kroeger, H.
Interactions of L-serine dehydratase from rat liver with its coenzyme and substrates
Biochim. Biophys. Acta
334
208-217
1974
Rattus norvegicus
-
Manually annotated by BRENDA team
Simon, D.; Hoshino, J.; Kroeger, H.
L-Serine dehydratase from rat liver. Purification and some properties
Biochim. Biophys. Acta
321
361-368
1973
Rattus norvegicus
Manually annotated by BRENDA team
Hoshino, J.; Simon, D.; Kroeger, H.
Influence of monovalent cations on the activity of L-serine (L-threonine) dehydratase from rat liver
Eur. J. Biochem.
27
388-394
1972
Rattus norvegicus
Manually annotated by BRENDA team
Pestana, A.; Sandoval, I.V.; Sols, A.
Inhibition by homocysteine of serine dehydratase and other pyridoxal 5'-phosphate enzymes of the rat through cofactor blockage
Arch. Biochem. Biophys.
146
373-379
1971
Rattus norvegicus
Manually annotated by BRENDA team
Hopgood, M.F.; Ballard, F.J.
The relative stability of liver cytosol enzymes incubated in vitro
Biochem. J.
144
371-376
1974
Rattus norvegicus
Manually annotated by BRENDA team
Suda, M.; Nakagawa, H.
L-Serine dehydratase (rat liver)
Methods Enzymol.
17B
346-351
1971
Rattus norvegicus
-
Manually annotated by BRENDA team
Ogawa, H.; Takasugawa, F.; Wakaki, K.; Kishi, H.; Eskandarian, M.R.; Kobayashi, M.; Date, T.; Huh, N.H.; Pitot, H.C.
Rat liver serine dehydratase. Bacterial expression and two folding domains as revealed by limited proteolysis
J. Biol. Chem.
274
12855-12860
1999
Rattus norvegicus
Manually annotated by BRENDA team
Yamada, T.; Komoto, J.; Takata, Y.; Ogawa, H.; Pitot, H.C.; Takusagawa, F.
Crystal structure of serine dehydratase from rat liver
Biochemistry
42
12854-12865
2003
Rattus norvegicus (P09367)
Manually annotated by BRENDA team
Imai, S.; Kanamoto, R.; Yagi, I.; Kotaru, M.; Saeki, T.; Iwami, K.
Response of the induction of rat liver serine dehydratase to changes in the dietary protein requirement
Biosci. Biotechnol. Biochem.
67
383-387
2003
Rattus norvegicus
Manually annotated by BRENDA team
Ogawa, H.; Gomi, T.; Takusagawa, F.; Masuda, T.; Goto, T.; Kan, T.; Huh, N.H.
Evidence for a dimeric structure of rat liver serine dehydratase
Int. J. Biochem. Cell Biol.
34
533-543
2002
Ovis aries, Rattus norvegicus
Manually annotated by BRENDA team
Xue, H.H.; Fujie, M.; Sakaguchi, T.; Oda, T.; Ogawa, H.; Kneer, N.M.; Lardy, H.A.; Ichiyama, A.
Flux of the L-serine metabolism in rat liver. The predominant contribution of serine dehydratase
J. Biol. Chem.
274
16020-16027
1999
Rattus norvegicus
Manually annotated by BRENDA team
Kanamoto, R.; Fujita, K.; Kumasaki, M.; Imai, S.; Kotaru, M.; Saeki, T.; Iwami, K.
Inverse correlation between the nitrogen balance and induction of rat liver serine dehydratase (SDH) by dietary protein
Biosci. Biotechnol. Biochem.
68
888-893
2004
Rattus norvegicus
Manually annotated by BRENDA team
Kashii, T.; Gomi, T.; Oya, T.; Ishii, Y.; Oda, H.; Maruyama, M.; Kobayashi, M.; Masuda, T.; Yamazaki, M.; Nagata, T.; Tsukada, K.; Nakajima, A.; Tatsu, K.; Mori, H.; Takusagawa, F.; Ogawa, H.; Pitot, H.C.
Some biochemical and histochemical properties of human liver serine dehydratase
Int. J. Biochem. Cell Biol.
37
574-589
2005
Rattus norvegicus, Homo sapiens (P20132), Homo sapiens
Manually annotated by BRENDA team
Lopez-Flores, I.; Barroso, J.B.; Valderrama, R.; Esteban, F.J.; Martinez-Lara, E.; Luque, F.; Peinado, M.A.; Ogawa, H.; Lupianez, J.A.; Peragon, J.
Serine dehydratase expression decreases in rat livers injured by chronic thioacetamide ingestion
Mol. Cell. Biochem.
268
33-43
2005
Rattus norvegicus
Manually annotated by BRENDA team
Lopez-Flores, I.; Peragon, J.; Valderrama, R.; Esteban, F.J.; Luque, F.; Peinado, M.A.; Aranda, F.; Lupianez, J.A.; Barroso, J.B.
Downregulation in the expression of the serine dehydratase in the rat liver during chronic metabolic acidosis
Am. J. Physiol.
291
R1295-R1302
2006
Rattus norvegicus
Manually annotated by BRENDA team
Zhong, B.; Sakai, S.; Saeki, T.; Kanamoto, R.
Excess leucine intake induces serine dehydratase in rat liver
Biosci. Biotechnol. Biochem.
71
2614-2617
2007
Rattus norvegicus (P09367)
Manually annotated by BRENDA team
Zhao, Z.; Liu, H.
A quantum mechanical/molecular mechanical study on the catalysis of the pyridoxal 5'-phosphate-dependent enzyme L-serine dehydratase
J. Phys. Chem. B
112
13091-13100
2008
Rattus norvegicus (P09367)
Manually annotated by BRENDA team
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