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Information on EC 4.3.1.18 - D-Serine ammonia-lyase and Organism(s) Escherichia coli and UniProt Accession P00926

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EC Tree
     4 Lyases
         4.3 Carbon-nitrogen lyases
             4.3.1 Ammonia-lyases
                4.3.1.18 D-Serine ammonia-lyase
IUBMB Comments
A pyridoxal-phosphate protein. The enzyme cleaves a carbon-oxygen bond, releasing a water molecule (hence the enzyme's original classification as EC 4.2.1.14, D-serine dehydratase) and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. Also acts, slowly, on D-threonine.
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Escherichia coli
UNIPROT: P00926
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
d-serine dehydratase, d-serine deaminase, dsdase, dsd1p, dsdsc, d-serine ammonia lyase, d-serine ammonia-lyase, d-serine dehydrase, d-ser dehydratase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-serine ammonia lyase
-
D-Serine deaminase
-
D-serine dehydratase
-
EC 4.2.1.14
formerly
D-Hydroxy amino acid dehydratase
-
-
-
-
D-Serine deaminase
D-Serine dehydrase
-
-
-
-
D-serine dehydratase
-
-
D-Serine hydrolase (deaminating)
-
-
-
-
Dehydratase, D-serine
-
-
-
-
Dsdase
-
-
-
-
Serine deaminase
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-Serine = pyruvate + NH3
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
SYSTEMATIC NAME
IUBMB Comments
D-serine ammonia-lyase (pyruvate-forming)
A pyridoxal-phosphate protein. The enzyme cleaves a carbon-oxygen bond, releasing a water molecule (hence the enzyme's original classification as EC 4.2.1.14, D-serine dehydratase) and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. Also acts, slowly, on D-threonine.
CAS REGISTRY NUMBER
COMMENTARY hide
9015-88-7
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-serine
pyruvate + NH3
show the reaction diagram
S-serine
pyruvate + NH3
show the reaction diagram
-
-
-
?
D-Allothreonine
?
show the reaction diagram
-
-
-
-
?
D-serine
?
show the reaction diagram
-
the enzyme enables cells to grow with D-Ser as the sole source of nitrogen
-
-
?
D-serine
pyruvate + NH3
show the reaction diagram
D-threonine
2-oxobutanoate + NH3
show the reaction diagram
-
-
-
-
?
L-allothreonine
?
show the reaction diagram
-
-
-
-
?
L-serine
pyruvate + NH3
show the reaction diagram
L-Thr
?
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
D-serine
pyruvate + NH3
show the reaction diagram
S-serine
pyruvate + NH3
show the reaction diagram
-
-
-
?
D-serine
?
show the reaction diagram
-
the enzyme enables cells to grow with D-Ser as the sole source of nitrogen
-
-
?
D-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
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
alkylamines
-
inactivation via a transimination of pyridoxal 5'-phosphate
DL-2,3-Diaminopropionic acid
-
-
DL-O-methyl serine
-
-
glycine
-
-
Isoserine
-
-
L-2,3-diaminopropionic acid
-
-
L-alanine
-
-
L-serine
-
-
O-methylserine
-
competitive
Tris
-
inactivation is prevented by the presence of sufficient K+ or NH4+ and less effectively by Na+ or pyridoxal 5'-phosphate
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-deoxymethylenephosphonate
-
can substitute for pyridoxal 5'-phosphate, the enzyme exhibits 35-40% of the activity of the native enzyme
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.1 - 4.9
D-allothreonine
0.086 - 1.68
D-Ser
0.1 - 0.35
D-serine
0.083 - 16
D-Thr
4 - 12.3
L-Ser
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.112 - 0.92
D-allothreonine
9.4 - 118
D-Ser
15.7
D-serine
-
-
0.95
D-Thr
-
pH 5.8, 25°C
1.8
L-allothreonine
-
pH 7.8, 25°C
0.12 - 0.153
L-Ser
17.2 - 19.6
L-Thr
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.46
Isoserine
-
0.035
DL-2,3-Diaminopropionic acid
-
25°C, pH 7.8
70
DL-O-methyl serine
-
25°C, pH 7.8
4.9
glycine
-
25°C, pH 7.8
0.33
Isoserine
-
25°C, pH 7.8
0.09
L-2,3-diaminopropionic acid
-
25°C, pH 7.8
17
L-alanine
-
25°C, pH 7.8
3
L-serine
-
25°C, pH 7.8
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.8 - 8
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9
-
pH 6.5: about 30% of maximal activity, pH 9.0: about 60% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
activity assay
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
47920
1 * 47920, calculated from amino acid sequence
37300
-
analytical ultracentrifugation
40000
-
sucrose density gradient centrifugation
47920
-
1 * 47920
48790
-
x * 48790, sequence analysis of peptides
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
?
-
x * 48790, sequence analysis of peptides
monomer
-
1 * 47920
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure is refined to 1.55 A resolution. Crystal structure of DSD reveals a larger pyridoxal 5'-phosphate-binding domain and a smaller domain
enzyme complexed with 3-amino-2-hydroxypropionate
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
G279D
-
mutant G279D and G281D, loss of activity, the mutant enzymes form a Schiff base linkage with pyridoxal 5'-phosphate but do not hold the cofactor in a catalytically competent orientation. G279D has 225fold reduced cofactor affinity, the ability to retain a cofactor:glycine complex is decreased 765fold. Mutant G281D has 50fold decreased cofactor affinity, the ability to retain a cofactor:glycine complex is decreased 1970fold
G281D
-
mutant G279D and G281D, loss of activity, the mutant enzymes form a Schiff base linkage with pyridoxal 5'-phosphate but do not hold the cofactor in a catalytically competent orientation. G279D has 225fold reduced cofactor affinity, the ability to retain a cofactor:glycine complex is decreased 765fold. Mutant G281D has 50fold decreased cofactor affinity, the ability to retain a cofactor:glycine complex is decreased 1970fold
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
6 h, 10% loss of activity
37
-
stable at and below, enzyme from mutant strain EM1610
50
-
enzyme from wild type strain EM1609 is stable, enzyme from mutant strain EM1610 is rapidly inactivated
54
-
1 min, dilute solution, complete loss of activity
55
-
enzyme from wild type strain is rapidly inactivated above
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
repeated freezing and thawing over a period of 1 or 2 months causes a 20-30% loss of activity
-
resolved completely by dialysis against L-Cys or D-Cys, reactivated by addition of pyridoxal 5'-phosphate
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0°C, stable almost indefinitely
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified from k12 mutant C6
-
to homogeneity
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expression in Saccharomyces cerevisiae
expression in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
molecular biology
the dsdA gene is used as a selectable marker for transformation of Arabidopsis
degradation
-
the enzyme is applied to remove endogenous D-serine from organotypic hippocampal slices. Complete removal of D-serine virtually abolishes NMDA-elicited neurotoxicity
medicine
-
loss of serine deaminase activity results in a hypercolonization phenotype, hypercolonization plays a role in urinary tract infections
pharmacology
-
the D-serine dehydratase gene is an excellent marker, especially in the construction of strains for which the use of antibiotic resistance genes as selective markers is not allowed
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Federiuk, C.S.; Bayer, R.; Shafer, J.A.
Characterization of the catalytic pathway for D-serine dehydratase
J. Biol. Chem.
258
5379-5385
1983
Escherichia coli
Manually annotated by BRENDA team
Federiuk, C.S.; Shafer, J.A.
A reaction pathway for transimination of the pyridoxal 5'-phosphate in D-serine dehydratase by amino acids
J. Biol. Chem.
258
5372-5378
1983
Escherichia coli
Manually annotated by BRENDA team
Schiltz, E.; Schmitt, W.
Sequence of Escherichia coli D-serine dehydratase
FEBS Lett.
134
57-62
1981
Escherichia coli
Manually annotated by BRENDA team
Federiuk, C.S.; Shafer, J.A.
Inactivation of D-serine dehydratase by alkylamines via a transimination of enzyme-linked cofactor
J. Biol. Chem.
256
7416-7423
1981
Escherichia coli
Manually annotated by BRENDA team
Schnackerz, K.D.; Ehrlich, J.H.; Giesemann, W.; Reed, T.A.
Mechanism of action of D-serine dehydratase. Identification of a transient intermediate
Biochemistry
18
3557-3563
1979
Escherichia coli
Manually annotated by BRENDA team
McFall, E.
Escherichia coli K-12 mutant forming a temperature-sensitive D-serine deaminase
J. Bacteriol.
121
1074-1077
1975
Escherichia coli
Manually annotated by BRENDA team
Robinson, W.G.; Labow, R.
D-Serine dehydratase (Escherichia coli)
Methods Enzymol.
17B
356-360
1971
Escherichia coli
-
Manually annotated by BRENDA team
Dupourque, D.; Newton, W.A.; Snell, E.E.
Purification and properties of D-serine dehydrase from Escherichia coli
J. Biol. Chem.
241
1233-1238
1966
Escherichia coli
Manually annotated by BRENDA team
Bloom, F.R.
Isolation and characterization of catabolite-resistant mutants in the D-serine deaminase system of Escherichia coli K-12
J. Bacteriol.
121
1085-1091
1975
Escherichia coli
Manually annotated by BRENDA team
Schackerz, K.D.; Feldmann, K.
Pyridoxal-5'-deoxymethylenephosphonate reconstituted D-serine dehydratase: a phosphorus-31 nuclear magnetic resonance study
Biochem. Biophys. Res. Commun.
95
1832-1838
1980
Escherichia coli
Manually annotated by BRENDA team
Marceau, M.; Lewis, S.D.; Shafer, J.A.
The glycine-rich region of Escherichia coli D-serine dehydratase. Altered interactions with pyridoxal 5'-phosphate produced by substitutions of aspartic acid for glycine
J. Biol. Chem.
263
16934-16941
1988
Escherichia coli
Manually annotated by BRENDA team
Pavlasova, E.; Stejskalova, E.; Sikyta, B.
Stability of hyperproduction of D-serine deaminase and tryptophanase in Escherichia coli
Biotechnol. Lett.
9
761-764
1987
Escherichia coli
-
Manually annotated by BRENDA team
Obmolova, G.; Tepliakov, A.; Harutyunyan, E.; Wahler, G.; Schnackerz, K.D.
Crystallization and preliminary X-ray studies of D-serine dehydratase from Escherichia coli
J. Mol. Biol.
214
641-642
1990
Escherichia coli
Manually annotated by BRENDA team
Maas, W.K.; Maas, R.; McFall, E.
D-Serine deaminase is a stringent selective marker in genetic crosses
J. Bacteriol.
177
459-461
1995
Escherichia coli
Manually annotated by BRENDA team
Schnackerz, K.D.; Tai, C.H.; Potsch, R.K.W.; Cook, P.F.
Substitution of pyridoxal 5'-phosphate in D-serine dehydratase from Escherichia coli by cofactor analogues provides information on cofactor binding and catalysis
J. Biol. Chem.
274
36935-36943
1999
Escherichia coli
Manually annotated by BRENDA team
Roesch, P.L.; Redford, P.; Batchelet, S.; Moritz, R.L.; Pellett, S.; Haugen, B.J.; Blattner, F.R.; Welch, R.A.
Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of the murine urinary tract
Mol. Microbiol.
49
55-67
2003
Escherichia coli
Manually annotated by BRENDA team
Schnackerz, K.D.; Keller, J.; Phillips, R.S.; Toney, M.D.
Ionization state of pyridoxal 5'-phosphate in d-serine dehydratase, dialkylglycine decarboxylase and tyrosine phenol-lyase and the influence of monovalent cations as inferred by (31)P NMR spectroscopy
Biochim. Biophys. Acta
1764
230-238
2006
Escherichia coli (P00926)
Manually annotated by BRENDA team
Shleper, M.; Kartvelishvily, E.; Wolosker, H.
D-Serine is the dominant endogenous coagonist for NMDA receptor neurotoxicity in organotypic hippocampal slices
J. Neurosci.
25
9413-9417
2005
Escherichia coli, Escherichia coli CFT073
Manually annotated by BRENDA team
Erikson, O.; Hertzberg, M.; Naesholm, T.
The dsdA gene from Escherichia coli provides a novel selectable marker for plant transformation
Plant Mol. Biol.
57
425-433
2005
Escherichia coli (P00926), Escherichia coli
Manually annotated by BRENDA team
Vorachek-Warren, M.K.; McCusker, J.H.
DsdA (D-serine deaminase): A new heterologous MX cassette for gene disruption and selection in Saccharomyces cerevisiae
Yeast
21
163-171
2004
Escherichia coli (P00926), Escherichia coli
Manually annotated by BRENDA team
Anfora, A.T.; Haugen, B.J.; Roesch, P.; Redford, P.; Welch, R.A.
Roles of serine accumulation and catabolism in the colonization of the murine urinary tract by Escherichia coli CFT073
Infect. Immun.
75
5298-5304
2007
Escherichia coli
Manually annotated by BRENDA team
Urusova, D.V.; Isupov, M.N.; Antonyuk, S.; Kachalova, G.S.; Obmolova, G.; Vagin, A.A.; Lebedev, A.A.; Burenkov, G.P.; Dauter, Z.; Bartunik, H.D.; Lamzin, V.S.; Melik-Adamyan, W.R.; Mueller, T.D.; Schnackerz, K.D.
Crystal structure of D-serine dehydratase from Escherichia coli
Biochim. Biophys. Acta
1824
422-432
2012
Escherichia coli (P00926), Escherichia coli
Manually annotated by BRENDA team