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Literature summary for 2.5.1.29 extracted from

  • Chang, T.H.; Guo, R.T.; Ko, T.P.; Wang, A.H.; Liang, P.H.
    Crystal structure of type-III geranylgeranyl pyrophosphate synthase from Saccharomyces cerevisiae and the mechanism of product chain length determination (2006), J. Biol. Chem., 281, 14991-15000.
    View publication on PubMed

Activating Compound

Activating Compound Comment Organism Structure
Triton X-100 activating at 0.1% Saccharomyces cerevisiae

Cloned(Commentary)

Cloned (Comment) Organism
expression of wild-type and mutant enzymes in Escheichia coli strain BL21(DE3) Saccharomyces cerevisiae

Crystallization (Commentary)

Crystallization (Comment) Organism
native and selenomethionine-labeled enzymes, hanging drop vapour diffusion method, mixing of 0.002 ml of the GGPP solution with 10–12 mg/ml protein in 25 mM Tris-HCl, pH 7.5, 150 mM NaCl, and 0.1% Triton X-100 with 0.002 ml of the mother liquor containing 0.08 M CH3COONa, 0.145 M (NH4)2SO4, 13% polyethylene glycol 4000, 7-9% glycerol, and 7-9% 1,2-propanediol, and equilibrating with 0.5 ml of the mother liquor, 7 days room temperature, X-ray diffraction structure determination and analysis at 1.98 A resolution Saccharomyces cerevisiae

Protein Variants

Protein Variants Comment Organism
F108A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
F108A/H139A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
H139A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
L135A/H139A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
additional information deletion of the first 9 or 17 amino acids caused the dissociation of dimer into monomer, the DELTA1-17 mutant shows abolished enzyme activity Saccharomyces cerevisiae
S71Y site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
Y107A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
Y107A/F108A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
Y107A/F108A//L135A/H139A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
Y107A/F108A/H139A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae
Y107A/H139A site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme Saccharomyces cerevisiae

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information kinetics of wild-type and mutant enzymes Saccharomyces cerevisiae
0.0004
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A/H139A Saccharomyces cerevisiae
0.0008
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant wild-type enzyme Saccharomyces cerevisiae
0.001
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A/L135A/H139A Saccharomyces cerevisiae
0.0011
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/H139A Saccharomyces cerevisiae
0.0017
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A Saccharomyces cerevisiae
0.0021
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant F108A Saccharomyces cerevisiae
0.0025
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant H139A Saccharomyces cerevisiae
0.0026
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A Saccharomyces cerevisiae
0.0027
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant F108A Saccharomyces cerevisiae
0.0027
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant L135A/H139A Saccharomyces cerevisiae
0.0032
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant wild-type enzyme Saccharomyces cerevisiae
0.0033
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A Saccharomyces cerevisiae
0.0047
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A Saccharomyces cerevisiae
0.0051
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant F108A/H139A Saccharomyces cerevisiae
0.0051
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant H139A Saccharomyces cerevisiae
0.017
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant L135A/H139A Saccharomyces cerevisiae
0.051
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A/L135A/H139A Saccharomyces cerevisiae
0.097
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A/H139A Saccharomyces cerevisiae
0.136
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant F108A/H139A Saccharomyces cerevisiae
0.267
-
isopentenyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/H139A Saccharomyces cerevisiae

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+
-
Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
trans,trans-farnesyl diphosphate + isopentenyl diphosphate Saccharomyces cerevisiae
-
diphosphate + geranylgeranyl diphosphate
-
?

Organism

Organism UniProt Comment Textmining
Saccharomyces cerevisiae
-
-
-

Reaction

Reaction Comment Organism Reaction ID
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate reaction mechanism and residues involved in substrate specificity and product chain lengt determination, overview Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
trans,trans-farnesyl diphosphate + isopentenyl diphosphate
-
Saccharomyces cerevisiae diphosphate + geranylgeranyl diphosphate
-
?
trans,trans-farnesyl diphosphate + isopentenyl diphosphate
-
Saccharomyces cerevisiae diphosphate + geranylgeranyl diphosphate product distribution of the wild-type and mutant enzymes, overview, mechanism of product chain length determination ?

Subunits

Subunits Comment Organism
More the enzyme structure is composed entirely of 15 alpha-helices joined by connecting loops and is arranged with alpha-helices around a large central cavity, the N-terminal 17 amino acids, 9-amino acid helix A and the following loop, of this GGPPs protrude from the helix core into the other subunit and contribute to the tight dimer formation, in each subunit, an elongated hydrophobic crevice surrounded by D, F, G, H, and I alpha-helices contains twoDDXXDmotifs at the top for substrate binding with one Mg2+ coordinated by Asp75, Asp79, and four water molecules. It is sealed at the bottom with three large residues of Tyr107, Phe108, and His139 Saccharomyces cerevisiae

Synonyms

Synonyms Comment Organism
short-chain type-III GGPP
-
Saccharomyces cerevisiae
type-III geranylgeranyl pyrophosphate synthase
-
Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Saccharomyces cerevisiae

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.6
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant F108A/H139A Saccharomyces cerevisiae
2.5
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant wild-type enzyme Saccharomyces cerevisiae
2.5
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A/H139A Saccharomyces cerevisiae
3.9
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/H139A Saccharomyces cerevisiae
4.2
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant H139A Saccharomyces cerevisiae
4.7
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant F108A Saccharomyces cerevisiae
4.9
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A Saccharomyces cerevisiae
5.6
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A Saccharomyces cerevisiae
6.4
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant L135A/H139A Saccharomyces cerevisiae
8.4
-
trans,trans-farnesyl diphosphate pH 7.5, 25°C, recombinant mutant Y107A/F108A/L135A/H139A Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Saccharomyces cerevisiae