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 | 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 | 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 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 | 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 | 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 | UniProt | Comment | Textmining |
---|---|---|---|
Escherichia coli | - |
- |
- |
Escherichia coli | P60472 | - |
- |
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 | 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 | Comment | Organism |
---|---|---|
undecaprenyl pyrophosphate synthase | - |
Escherichia coli |
UPPs | - |
Escherichia coli |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
25 | - |
assay at | Escherichia coli |
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 Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.5 | - |
assay at | Escherichia coli |
Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
---|---|---|---|---|---|
1.1 | - |
Mg2+ | pH 7.5, 25°C | Escherichia coli |
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 |