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Literature summary for 2.5.1.31 extracted from

  • Guo, R.T.; Ko, T.P.; Chen, A.P.; Kuo, C.J.; Wang, A.H.; Liang, P.H.
    Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis (2005), J. Biol. Chem., 280, 20762-20774.
    View publication on PubMed

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant wild-type and mutant D26A enzymes in complex with Mg2+, isopentenyl diphosphate and substrate analogue farnesyl thiodiphosphate, protein solution containing 10 mg/ml protein in 25 mM Tris-HCl, pH 7.5, 150 mM NaCl, and 0.03% Triton X-100, is mixed with dried MgCl2 and isopentenyl diphosphate powder, hanging drop vapour diffusion method, 0.002 ml of the final protein solution with equal volume of mother liquor containing 20% ethylene glycol, 2-5% PEG 35000, equilibration against 0.5 ml mother liquor at room temperature, 2 days, soaking in cryoprotectant containing 2.5 mM MgCl2, 2.5 mM isopentenyl diphosphate, 30% ethylene glycol, and 5% PEG 35000 for 1 day, X-ray diffraction strcture determination and analysis at 1.9-2.2 A resolution, molecular modeling Escherichia coli

Protein Variants

Protein Variants Comment Organism
D26A site-directed mutagenesis, altered Mg2+ binding and about 1000fold reduced activity compared to the wild-type enzyme Escherichia coli
D26E site-directed mutagenesis, altered Mg2+ binding and over 10000fold reduced activity compared to the wild-type enzyme Escherichia coli
D26K site-directed mutagenesis, altered Mg2+ binding and about 10000fold reduced activity compared to the wild-type enzyme Escherichia coli
D26R site-directed mutagenesis, altered Mg2+ binding and over 10000fold reduced activity compared to the wild-type enzyme Escherichia coli

Inhibitors

Inhibitors Comment Organism Structure
farnesyl thiodiphosphate
-
Escherichia coli
Mg2+ inhibitory at high concentrations of e.g. 50 mM; inhibitory at high concentrations of e.g. 50 mM Escherichia coli

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.00037
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 1 mM MgCl2 Escherichia coli
0.0004
-
farnesyl diphosphate pH 7.5, 25°C, wild-type enzyme Escherichia coli
0.00041
-
isopentenyl diphosphate pH 7.5, 25°C, wild-type enzyme Escherichia coli
0.00044
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 3 mM MgCl2 Escherichia coli
0.00046
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26K Escherichia coli
0.00046
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26K mutant with 0.5 mM MgCl2 Escherichia coli
0.0005
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26A Escherichia coli
0.00055
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26R Escherichia coli
0.00055
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26R mutant with 0.5 mM MgCl2 Escherichia coli
0.00067
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26E Escherichia coli
0.00067
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26E mutant with 0.5 mM MgCl2 Escherichia coli
0.0009
-
isopentenyl diphosphate pH 7.5, 25°C, mutant D26K Escherichia coli
0.0014
-
isopentenyl diphosphate pH 7.5, 25°C, mutant D26A Escherichia coli
0.0015
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 0.05 mM MgCl2 Escherichia coli
0.00157
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 50 mM MgCl2 Escherichia coli
0.0021
-
isopentenyl diphosphate pH 7.5, 25°C, mutant D26E Escherichia coli
0.0022
-
isopentenyl diphosphate pH 7.5, 25°C, mutant D26R Escherichia coli
0.0092
-
isopentenyl diphosphate pH 7.5, 25°C, D26K mutant with 0.5 mM MgCl2 Escherichia coli
0.0097
-
isopentenyl diphosphate pH 7.5, 25°C, wild type with 1 mM MgCl2 Escherichia coli
0.0115
-
isopentenyl diphosphate pH 7.5, 25°C, wild type with 0.05 mM MgCl2 Escherichia coli
0.0175
-
isopentenyl diphosphate pH 7.5, 25°C, wild type with 3 mM MgCl2 Escherichia coli
0.0208
-
isopentenyl diphosphate pH 7.5, 25°C, D26E mutant with 0.5 mM MgCl2 Escherichia coli
0.0223
-
isopentenyl diphosphate pH 7.5, 25°C, D26R mutant with 0.5 mM MgCl2 Escherichia coli
0.291
-
isopentenyl diphosphate pH 7.5, 25°C, wild type with 50 mM MgCl2 Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ role of the metal ion in catalysis, required for binding of isopentenyl diphosphate to the enzyme, best at 1 mM, low activity at 50 mM, Asp26 is required for efficient binding, Mg2+ is bound to the diphosphate of farnesyl diphosphate in the wild-type enzyme, but to the diphosphate of isopentenyl diphosphate in the mutant D26A, Mg2+ is not required for the overall structure stability, overview Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
farnesyl diphosphate + isopentenyl diphosphate Escherichia coli consecutive condensation of 8 molecules of isopentenyl diphosphate with farnesyl diphosphate to form the lipid carrier undecaprenyl diphosphate to mediate bacterial peptidoglycan synthesis diphosphate + di-trans-poly-cis-undecaprenyl diphosphate
-
?
additional information Escherichia coli catalyzes the consecutive condensation reactions of a farnesyl diphosphate (FPP) with eight isopentenyl diphosphates (IPP), in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall ?
-
?

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
-
-
Escherichia coli P60472
-
-

Reaction

Reaction Comment Organism Reaction ID
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate active site structure, detailed catalytic mechanism, substrate binding mechanism, D26, H43, S71, N74, and R77 are involved Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate
-
Escherichia coli 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate
-
?
farnesyl diphosphate + isopentenyl diphosphate consecutive condensation of 8 molecules of isopentenyl diphosphate with farnesyl diphosphate to form the lipid carrier undecaprenyl diphosphate to mediate bacterial peptidoglycan synthesis Escherichia coli diphosphate + di-trans-poly-cis-undecaprenyl diphosphate
-
?
farnesyl diphosphate + isopentenyl diphosphate stereochemistry of the reaction Escherichia coli diphosphate + di-trans-poly-cis-undecaprenyl diphosphate
-
?
additional information catalyzes the consecutive condensation reactions of a farnesyl diphosphate (FPP) with eight isopentenyl diphosphates (IPP), in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall Escherichia coli ?
-
?

Synonyms

Synonyms Comment Organism
undecaprenyl pyrophosphate synthase
-
Escherichia coli
UPPs
-
Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Escherichia coli

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.00006
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26R Escherichia coli
0.0000633
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26R mutant with 0.5 mM MgCl2 Escherichia coli
0.0000766
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26K mutant with 0.5 mM MgCl2 Escherichia coli
0.00008
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26K Escherichia coli
0.000366
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26E mutant with 0.5 mM MgCl2 Escherichia coli
0.0004
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26E Escherichia coli
0.0033
-
farnesyl diphosphate pH 7.5, 25°C, mutant D26A Escherichia coli
1.23
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 0.05 mM MgCl2 Escherichia coli
1.92
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 3 mM MgCl2 Escherichia coli
1.98
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 1 mM MgCl2 Escherichia coli
2.5
-
farnesyl diphosphate pH 7.5, 25°C, wild-type enzyme Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Escherichia coli

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
1.1
-
Mg2+ pH 7.5, 25°C Escherichia coli

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.1151
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26R mutant with 0.5 mM MgCl2 Escherichia coli
0.1665
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26K mutant with 0.5 mM MgCl2 Escherichia coli
0.5462
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, D26E mutant with 0.5 mM MgCl2 Escherichia coli
820
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 0.05 mM MgCl2 Escherichia coli
4363
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 3 mM MgCl2 Escherichia coli
5351
-
(2E,6E)-farnesyl diphosphate pH 7.5, 25°C, wild type with 1 mM MgCl2 Escherichia coli