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EC Tree
IUBMB Comments The enzyme catalyses a step in the biosynthetic pathway of 2-aminoethylphosphonate, a component of the capsular polysaccharide complex of Bacteroides fragilis. Requires thiamine diphosphate and Mg2+ as cofactors. The enzyme is activated by the divalent cations Mg2+, Ca2+ and Mn2+. Pyruvate and sulfopyruvate can also act as substrates, but more slowly. This enzyme drives the reaction catalysed by EC 5.4.2.9, phosphoenolpyruvate mutase, in the thermodynamically unfavourable direction of 3-phosphonopyruvate formation . It is the initial step in all of the major biosynthetic pathways of phosphonate natural products .
The enzyme appears in viruses and cellular organisms
Synonyms
PnPy decarboxylase, Ppd, PPDC, Ppyr decarboxylase,
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PnPy decarboxylase
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Ppd
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Ppd
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
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-
PPDC
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PPDC
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
-
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3-phosphonopyruvate = 2-phosphonoacetaldehyde + CO2
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3-phosphonopyruvate carboxy-lyase (2-phosphonoacetaldehyde-forming)
The enzyme catalyses a step in the biosynthetic pathway of 2-aminoethylphosphonate, a component of the capsular polysaccharide complex of Bacteroides fragilis. Requires thiamine diphosphate and Mg2+ as cofactors. The enzyme is activated by the divalent cations Mg2+, Ca2+ and Mn2+. Pyruvate and sulfopyruvate can also act as substrates, but more slowly. This enzyme drives the reaction catalysed by EC 5.4.2.9, phosphoenolpyruvate mutase, in the thermodynamically unfavourable direction of 3-phosphonopyruvate formation [2]. It is the initial step in all of the major biosynthetic pathways of phosphonate natural products [3].
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3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
pyruvate
acetaldehyde + CO2
0.5% of 3-phosphonopyruvate kcat
-
-
?
sulfopyruvate
sulfoacetaldehyde + CO2
0.5% of 3-phosphonopyruvate kcat
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-
?
additional information
?
-
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
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-
-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
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-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
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-
-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
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-
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ir
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
key enzyme in the biosynthesis of C-P bond compounds, overview
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ir
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
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-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
-
-
?
additional information
?
-
neither pyruvate, beta-hydroxypyruvate, nor fluoropyruvate serve as alternative substrates
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?
additional information
?
-
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
neither pyruvate, beta-hydroxypyruvate, nor fluoropyruvate serve as alternative substrates
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?
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3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
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-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
-
-
-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
key enzyme in the biosynthesis of C-P bond compounds, overview
-
-
ir
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
-
-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
-
-
?
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thiamine diphosphate
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-
thiamine diphosphate
dependent on
thiamine diphosphate
primary sequence of Ppd contains signature typical for enzymes requiring thiamine diphosphate
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Ca2+
required for activity
Ca2+
Ca2+ can substitute for Mg2+
Mg2+
required for activity
Mg2+
-
required for activity
Mg2+
Mg2+ is required for activity, Ca2+ and Mn2+ can substitute for Mg2+
Mn2+
required for activity
Mn2+
Mn2+ can substitute for Mg2+
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phosphonodifluoropyruvate
-
mechanism-based inhibitor, irreversibly inactivates the enzyme, accompanied by release of fluoride ion
sulfopyruvate
competitive inhibition
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0.0029 - 3.02
3-phosphonopyruvate
0.013
thiamine diphosphate
25°C, pH 7.3
0.0029
3-phosphonopyruvate
-
pH 7.0, 30°C
0.0032
3-phosphonopyruvate
25°C, pH 7.3, 5 mM MgCl2, 1 mM MnCl2, 0.2 mM thiamine pyrophosphate
0.0032
3-phosphonopyruvate
wild type enzyme, at pH 8.0 (HEPES buffer) and at 30°C
0.013
3-phosphonopyruvate
mutant enzyme H111A, at pH 8.0 (HEPES buffer) and at 30°C
0.04
3-phosphonopyruvate
mutant enzyme D297E, at pH 8.0 (HEPES buffer) and at 30°C
0.25
3-phosphonopyruvate
mutant enzyme S25N, at pH 8.0 (HEPES buffer) and at 30°C
1.47
3-phosphonopyruvate
mutant enzyme S25D, at pH 8.0 (HEPES buffer) and at 30°C
3.02
3-phosphonopyruvate
mutant enzyme D297N, at pH 8.0 (HEPES buffer) and at 30°C
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0.31 - 10.2
3-phosphonopyruvate
0.31
3-phosphonopyruvate
mutant enzyme S25D, at pH 8.0 (HEPES buffer) and at 30°C
0.55
3-phosphonopyruvate
mutant enzyme D297N, at pH 8.0 (HEPES buffer) and at 30°C
0.76
3-phosphonopyruvate
mutant enzyme D297E, at pH 8.0 (HEPES buffer) and at 30°C
0.78
3-phosphonopyruvate
mutant enzyme S25N, at pH 8.0 (HEPES buffer) and at 30°C
1.18
3-phosphonopyruvate
wild type enzyme, at pH 8.0 (HEPES buffer) and at 30°C
1.24
3-phosphonopyruvate
mutant enzyme H111A, at pH 8.0 (HEPES buffer) and at 30°C
10.1
3-phosphonopyruvate
-
pH 7.0, 30°C
10.2
3-phosphonopyruvate
25°C, pH 7.3, 5 mM MgCl2, 1 mM MnCl2, 0.2 mM thiamine diphosphate
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0.2
sulfopyruvate
25°C, pH 7.0
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strain Tü494
Swissprot
brenda
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
strain Tü494
Swissprot
brenda
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swissprot
brenda
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-
brenda
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-
brenda
gene bcpC
SwissProt
brenda
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36000
-
4 * 36000, SDS-PAGE
40000
3 * 40000, SDS-PAGE
41000
x * 41000, deduced from nucleotide sequence
41199
3 * 41199, MALDI-TOF mass spectroscopy
43600
2 * 43600, gel filtration
46000
2 * 46000, gel filtration
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tetramer
-
4 * 36000, SDS-PAGE
?
x * 41000, deduced from nucleotide sequence
?
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
x * 41000, deduced from nucleotide sequence
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homodimer
2 * 43600, gel filtration
homodimer
2 * 46000, gel filtration
homodimer
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
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2 * 43600, gel filtration
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homodimer
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
2 * 46000, gel filtration
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trimer
3 * 40000, SDS-PAGE
trimer
3 * 41199, MALDI-TOF mass spectroscopy
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D258A
9% of wild-type kcat for 3-phosphonopyruvate
D260A
0.1% of wild-type kcat for 3-phosphonopyruvate
E213A
5% of wild-type kcat for 3-phosphonopyruvate
D297E
catalytic turnover rate is 1.5fold less and Km is increased about 13fold compared to the wild type enzyme
D297N
catalytic turnover rate of D297N is 2fold lower and Km is increased 940fold compared to the wild type enzyme
G94A
compared to wild type PPDC, Km is increased only 2fold, while kcat is 4fold lower
H110A
no detectable activity
H111A
the mutation has no significant influence on the steady state kinetic constants compared to the wild type enzyme
S25D
catalytic turnover rate is 4fold less and Km is increased 460fold compared to the wild type enzyme
S25N
catalytic turnover rate is 1.5fold less and Km is increased 80fold compared to the wild type enzyme
D297N
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
catalytic turnover rate of D297N is 2fold lower and Km is increased 940fold compared to the wild type enzyme
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G94A
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
compared to wild type PPDC, Km is increased only 2fold, while kcat is 4fold lower
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H110A
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
no detectable activity
-
H111A
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
the mutation has no significant influence on the steady state kinetic constants compared to the wild type enzyme
-
S25D
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
-
catalytic turnover rate is 4fold less and Km is increased 460fold compared to the wild type enzyme
-
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-20°C and 4°C, half-life of 50 days
4°C, 50 mM Tris-HCl, pH 7.5, 3 weeks, no loss of activity
-
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ammonium sulfate, DEAE-cellulose, TSK-gel Phenyl-5PW, gel filtration, Mono Q
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Ni-NTA column chromatography
recombinant Ppyr decarboxylase, ammonium sulfate, DEAE-Sepahrose, hydroxylapatite
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expressed as a recombinant fusion protein with an N-terminal 10x histidine-tag in Escherichia coli BL21(DE3) cells
expression in Escherichia coli
gene bcpC, located in the bialaphos biosynthetic gene cluster, DNA and amino acid sequence determination and analysis, complementation of an enzyme-deficient mutant strain of Streptomyces wedmorensis NP-7, enzyme expression in Streptomyces lividans
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Nakashita, H.; Kozuka, K.; Hidaka, T.; Hara, O.; Seto, H.
Identification and expression of the gene encoding phosphonopyruvate decarboxylase of Streptomyces hygroscopicus
Biochim. Biophys. Acta
1490
159-162
2000
Streptomyces hygroscopicus (Q54271), Streptomyces hygroscopicus
brenda
Schwartz, D.; Recktenwald, J.; Pelzer, S.; Wohlleben, W.
Isolation and characterization of the PEP-phosphomutase and the phosphonopyruvate decarboxylase genes from the phosphinothricin tripeptide producer Streptomyces viridochromogenes Tu494
FEMS Microbiol. Lett.
163
149-157
1998
Streptomyces viridochromogenes (O86938), Streptomyces viridochromogenes, Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494 (O86938)
brenda
Nakashita, H.; Watanabe, K.; Hara, O.; Hidaka, T.; Seto, H.
Studies on the biosynthesis of bialaphos. Biochemical mechanism of C-P bond formation: discovery of phosphonopyruvate decarboxylase which catalyzes the formation of phosphonoacetaldehyde from phosphonopyruvate
J. Antibiot.
50
212-219
1997
Streptomyces hygroscopicus
brenda
Zhang, G.; Dai, J.; Lu, Z.; Dunaway-Mariano, D.
The phosphonopyruvate decarboxylase from Bacteroides fragilis
J. Biol. Chem.
278
41302-41308
2003
Bacteroides fragilis (Q9F768), Bacteroides fragilis
brenda
Johnen, S.; Sprenger, G.
Characterization of recombinant thiamine diphosphate-dependent phosphonopyruvate decarboxylase from Streptomyces viridochromogenes Tü494
J. Mol. Catal. B
61
39-46
2009
Streptomyces viridochromogenes (O86938), Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494 (O86938)
-
brenda
Pallitsch, K.; Rogers, M.P.; Andrews, F.H.; Hammerschmidt, F.; McLeish, M.J.
Phosphonodifluoropyruvate is a mechanism-based inhibitor of phosphonopyruvate decarboxylase from Bacteroides fragilis
Bioorg. Med. Chem.
25
4368-4374
2017
Bacteroides fragilis
brenda
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4.1.1.82 phosphonopyruvate decarboxylase
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