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Information on EC 4.1.1.82 - phosphonopyruvate decarboxylase for references in articles please use BRENDA:EC4.1.1.82
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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, 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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-
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3-phosphonopyruvate = 2-phosphonoacetaldehyde + CO2
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-
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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
-
-
?
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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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
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-
-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494
/ Tu 494
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-
-
-
?
additional information
?
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-
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
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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
Q9F768
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-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
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-
-
?
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
Q54271
key enzyme in the biosynthesis of C-P bond compounds, overview
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-
ir
3-phosphonopyruvate
2-phosphonoacetaldehyde + CO2
O86938
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-
-
?
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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primary sequence of Ppd contains signature typical for enzymes requiring thiamine diphosphate
thiamine diphosphate
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dependent on
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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
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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
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mutant enzyme D297E, at pH 8.0 (HEPES buffer) and at 30°C
0.25
3-phosphonopyruvate
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mutant enzyme S25N, at pH 8.0 (HEPES buffer) and at 30°C
1.47
3-phosphonopyruvate
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mutant enzyme S25D, at pH 8.0 (HEPES buffer) and at 30°C
3.02
3-phosphonopyruvate
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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
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mutant enzyme S25D, at pH 8.0 (HEPES buffer) and at 30°C
0.55
3-phosphonopyruvate
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mutant enzyme D297N, at pH 8.0 (HEPES buffer) and at 30°C
0.76
3-phosphonopyruvate
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mutant enzyme D297E, at pH 8.0 (HEPES buffer) and at 30°C
0.78
3-phosphonopyruvate
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mutant enzyme S25N, at pH 8.0 (HEPES buffer) and at 30°C
1.18
3-phosphonopyruvate
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wild type enzyme, at pH 8.0 (HEPES buffer) and at 30°C
1.24
3-phosphonopyruvate
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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
-
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
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4 * 36000, SDS-PAGE
trimer
3 * 40000, SDS-PAGE; 3 * 41199, MALDI-TOF mass spectroscopy
?
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x * 41000, deduced from nucleotide sequence
?
Streptomyces viridochromogenes DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494 / Tu 494
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x * 41000, deduced from nucleotide sequence
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homodimer
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2 * 43600, gel filtration; 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; 2 * 46000, gel filtration
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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
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catalytic turnover rate is 1.5fold less and Km is increased about 13fold compared to the wild type enzyme
D297N
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catalytic turnover rate of D297N is 2fold lower and Km is increased 940fold compared to the wild type enzyme
G94A
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compared to wild type PPDC, Km is increased only 2fold, while kcat is 4fold lower
H110A
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no detectable activity
H111A
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the mutation has no significant influence on the steady state kinetic constants compared to the wild type enzyme
S25D
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catalytic turnover rate is 4fold less and Km is increased 460fold compared to the wild type enzyme
S25N
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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
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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
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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
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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
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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
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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, Bacteroides fragilis (Q9F768)
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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