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Information on EC 4.3.1.17 - L-serine ammonia-lyase and Organism(s) Legionella pneumophila and UniProt Accession Q5ZXE1

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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:
Legionella pneumophila
UNIPROT: Q5ZXE1
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The taxonomic range for the selected organisms is: Legionella pneumophila
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
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L-serine
=
pyruvate
+
NH3
=
+
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
L-serine dehydratase
-
Dehydratase, L-serine
-
-
-
-
L-Hydroxy amino acid dehydratase
-
-
-
-
L-SD
-
-
-
-
L-SD1
-
-
-
-
L-SD2
-
-
-
-
L-Serine deaminase
-
-
-
-
SD
-
-
-
-
SDH
-
-
-
-
Serine deaminase
-
-
-
-
Serine dehydratase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-serine = pyruvate + NH3
show the reaction diagram
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
-
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-Ser
pyruvate + NH3
show the reaction diagram
-
-
-
ir
L-serine
pyruvate + NH3
show the reaction diagram
L-Thr
2-oxobutanoate + NH3
show the reaction diagram
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
-
-
?
L-serine
pyruvate + NH3
show the reaction diagram
-
-
-
-
?
additional information
?
-
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
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4Fe-4S-center
the enzyme contains a [4Fe-4S]2+ cluster that acts as a Lewis acid to extract the hydroxyl group of L-serine during the dehydration reaction. Fe-S cluster binding induces protein conformational changes in L-serine dehydratase. All four iron atoms of the [4Fe-4S] cluster are coordinated with protein cysteine residues (C396, C485, C343, C385). formation of disulfide bonds between C396 and C485 and possibly between C343 and C385
K+
addition results in weak activation
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ammonia
product inhibition, noncompetitive
D-serine
competitive
L-cysteine
competitive
oxygen
lpLSD is weakly sensitive to oxygen
pyruvate
product inhibition, competitive
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2 - 17.8
L-Ser
1.7 - 189
L-serine
4.3
L-serine
-
pH 7, temperature not specified in the publication
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
323 - 512
L-Ser
4.07 - 512
L-serine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
18 - 230
L-Ser
1.3 - 165
L-serine
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
10
D-serine
pH 7.0, temperature not specified in the publication
0.1
L-cysteine
pH 7.0, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
49476
49480
-
gel filtration, monomer
98950
-
gel filtration, dimer
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
gel filtration, 2 * 49476, only dimer displays catalytic activity. In the absence of substrate, lpLSD is predominately a dimer
monomer
-
gel filtration, 1 * 49476, monomeric form does not possess enzymatic activity
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
DELTA(C458)
mutant enzyme has no detectable activity
DELTA(P456,E457,C458)
mutant enzyme has no detectable activity
E445A
mutant enzyme has no detectable activity
E457A
kcat/Km for L-serine is 1.5fold lower than the wild-type value
H124A/N126A
kcat/Km for L-serine is 48.5fold lower than the wild-type value
H19A
kcat/Km for L-serine is 127fold lower than the wild-type value
H61A
mutant enzyme has no detectable activity
H61N
mutant enzyme has no detectable activity
H61S
mutant enzyme has no detectable activity
K444A
mutant enzyme has no detectable activity
S16A
mutant enzyme has no detectable activity
S17A
kcat/Km for L-serine is 4.8fold lower than the wild-type value
S18A
mutant enzyme has no detectable activity
S53A
kcat/Km for L-serine is 2.9fold lower than the wild-type value
T20A
kcat/Km for L-serine is 4.2fold lower than the wild-type value
T290A
kcat/Km for L-serine is 127fold lower than the wild-type value
T446A
kcat/Km for L-serine is 91.7fold lower than the wild-type value
T57A
kcat/Km for L-serine is 31.7fold lower than the wild-type value
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
using cobalt-based affinity columns
using cobalt-based Talon immobilized metal affinity columns
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli as a His-tagged fusion protein
expression in Escherichia coli BL21 DE3
expressed in Escherichia coli as a His-tagged fusion protein
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
development of a simple, direct, and continuous assay based on the absorbance of pyruvate, the product of the dehydratase reaction
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Xu, X.L.; Chen, S.; Grant, G.A.
Kinetic, mutagenic, and structural homology analysis of L-serine dehydratase from Legionella pneumophila
Arch. Biochem. Biophys.
515
28-36
2011
Legionella pneumophila (Q5ZXE1), Legionella pneumophila
Manually annotated by BRENDA team
Chen, S.; Xu, X.L.; Grant, G.A.
Allosteric activation and contrasting properties of L-serine dehydratase types 1 and 2
Biochemistry
51
5320-5328
2012
Bacillus subtilis, Legionella pneumophila (Q5ZXE1), Legionella pneumophila
Manually annotated by BRENDA team
Grant, G.A.
Kinetic evidence of a noncatalytic substrate binding site that regulates activity in Legionella pneumophila L-serine dehydratase
Biochemistry
51
6961-6967
2012
Legionella pneumophila
Manually annotated by BRENDA team
Xu, X.L.; Grant, G.A.
Mutagenic and chemical analyses provide new insight into enzyme activation and mechanism of the type 2 iron-sulfur L-serine dehydratase from Legionella pneumophila
Arch. Biochem. Biophys.
596
108-117
2016
Legionella pneumophila (Q5ZXE1), Legionella pneumophila
Manually annotated by BRENDA team
Yan, Y.; Grant, G.A.; Gross, M.L.
Hydrogen-deuterium exchange mass spectrometry reveals unique conformational and chemical transformations occurring upon [4Fe-4S] cluster binding in the type 2 L-serine dehydratase from Legionella pneumophila
Biochemistry
54
5322-5328
2015
Legionella pneumophila (Q5ZXE1), Legionella pneumophila
Manually annotated by BRENDA team