Literature summary for 2.5.1.31 extracted from

Chang, S.Y.; Ko, T.P.; Liang, P.H.; Wang, A.H.
Catalytic mechanism revealed by the crystal structure of undecaprenyl pyrophosphate synthase in complex with sulfate, magnesium, and triton (2003), J. Biol. Chem., 278, 29298-29307.

Activating Compound

Activating Compound	Comment	Organism	Structure
Triton X-100	1.5% v/v, 2 molecules are bound in the active site tunnel of the beta-subunit, binding structure	Escherichia coli

Cloned(Commentary)

Cloned (Comment)	Organism
overexpression of His-tagged wild-type and mutant enzymes	Escherichia coli

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified His-tagged wild-type enzyme in complex with Mg2+, sulfates, and 2 molecules of Triton X-100, hanging drop vapour diffusion method, 0.002 ml protein solution containing 10 mg/ml protein, 2% Triton X-100, 5 mM MgCl2, and 0.66 mM farnesyl diphosphate, is mixed with equal volume of mother liquid containing 0.01 M CoCl2, 0.1 M MES, pH 6.5, and 1.8 M ammonium sulfate, equilibration against 0.2 ml mother liquid at 25°C, 10 days, X-ray diffraction structure determination and analysis at 1.73 A resolution, modeling	Escherichia coli

Crystallization (Comment)

Organism

purified His-tagged wild-type enzyme in complex with Mg2+, sulfates, and 2 molecules of Triton X-100, hanging drop vapour diffusion method, 0.002 ml protein solution containing 10 mg/ml protein, 2% Triton X-100, 5 mM MgCl2, and 0.66 mM farnesyl diphosphate, is mixed with equal volume of mother liquid containing 0.01 M CoCl2, 0.1 M MES, pH 6.5, and 1.8 M ammonium sulfate, equilibration against 0.2 ml mother liquid at 25°C, 10 days, X-ray diffraction structure determination and analysis at 1.73 A resolution, modeling

Escherichia coli

Protein Variants

Protein Variants	Comment	Organism
D26A	site-directed mutagenesis, reduced activity compared to the wild-type enzyme	Escherichia coli
E213A	site-directed mutagenesis, reduced activity compared to the wild-type enzyme	Escherichia coli
H199A	site-directed mutagenesis, activity is similar to the wild-type enzyme	Escherichia coli
H199A/E213A	site-directed mutagenesis, reduced activity compared to the wild-type enzyme	Escherichia coli
H43A	site-directed mutagenesis, reduced activity compared to the wild-type enzyme	Escherichia coli

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
additional information	-	additional information	steady-state kinetics	Escherichia coli
0.00028	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, H199A mutant	Escherichia coli
0.0003	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A	Escherichia coli
0.0004	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, wild type	Escherichia coli
0.0004	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant wild-type enzyme	Escherichia coli
0.0005	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant D26A	Escherichia coli
0.0005	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, D26A mutant	Escherichia coli
0.00066	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A/E213A	Escherichia coli
0.00066	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, H199A/E213A mutant	Escherichia coli
0.0007	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant E213A	Escherichia coli
0.0007	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, E213A mutant	Escherichia coli
0.003	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H43A	Escherichia coli
0.003	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, H43A mutant	Escherichia coli
0.004	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant wild-type enzyme	Escherichia coli
0.0041	-	isopentenyl diphosphate	pH 7.5, 25°C, wild type	Escherichia coli
0.014	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant D26A	Escherichia coli
0.0141	-	isopentenyl diphosphate	pH 7.5, 25°C, D26A mutant	Escherichia coli
0.016	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A	Escherichia coli
0.016	-	isopentenyl diphosphate	pH 7.5, 25°C, H199A mutant	Escherichia coli
0.063	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant H43A	Escherichia coli
0.063	-	isopentenyl diphosphate	pH 7.5, 25°C, H43A mutant	Escherichia coli
0.279	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A/E213A	Escherichia coli
0.279	-	isopentenyl diphosphate	pH 7.5, 25°C, H199A/E213A mutant	Escherichia coli
0.28	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant E213A	Escherichia coli
0.28	-	isopentenyl diphosphate	pH 7.5, 25°C, E213A mutant	Escherichia coli

Metals/Ions

Metals/Ions	Comment	Organism
KCl	activates at 50 mM	Escherichia coli
Mg2+	required, best at 0.5 mM MgCl2, 2 Mg2+ are bound at the subunit interface, binding structure	Escherichia coli
Mg2+	is chelated by His199 and Glu213 from different subunits and possibly plays astructural rather than catalytic role	Escherichia coli
sulfate	2 molecules bound per enzyme dimer, 1 at each active site, binding structure	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	-	?

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant HIs-tagged wild-type and mutant enzymes	Escherichia coli

Reaction

Reaction	Comment	Organism	Reaction ID
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate	active site structure and catalytic mechanism	Escherichia coli	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
(2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate	-	Escherichia coli	8 diphosphate + ditrans,octacis-undecaprenyl diphosphate	-	?
di-trans-poly-cis-decaprenyl diphosphate + isopentenyl diphosphate	di-trans-poly-cis-decaprenyl diphosphate is farnesyl diphosphate	Escherichia coli	diphosphate + di-trans-poly-cis-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	-	?

Subunits

Subunits	Comment	Organism
dimer	alphabeta	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
0.0025	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A/E213A	Escherichia coli
0.0025	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A/E213A	Escherichia coli
0.0025	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A/E213A	Escherichia coli
0.0026	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H43A and mutant E213A	Escherichia coli
0.0026	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant H43A and mutant E213A	Escherichia coli
0.0026	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H43A and mutant E213A	Escherichia coli
0.0033	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant D26A	Escherichia coli
0.0033	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant D26A	Escherichia coli
0.0033	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant D26A	Escherichia coli
2.2	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A	Escherichia coli
2.2	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A	Escherichia coli
2.2	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A	Escherichia coli
2.5	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant wild-type enzyme	Escherichia coli
2.5	-	isopentenyl diphosphate	pH 7.5, 25°C, recombinant wild-type enzyme	Escherichia coli
2.5	-	farnesyl diphosphate	pH 7.5, 25°C, recombinant wild-type enzyme	Escherichia coli

pH Optimum

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

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
0.866	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H43A	Escherichia coli
3.79	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A/E213A	Escherichia coli
6.25	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant wild-type enzyme	Escherichia coli
6.6	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant D26A	Escherichia coli
7.86	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant H199A	Escherichia coli
37.14	-	(2E,6E)-farnesyl diphosphate	pH 7.5, 25°C, recombinant mutant E213A	Escherichia coli