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Information on EC 2.5.1.29 - geranylgeranyl diphosphate synthase and Organism(s) Saccharomyces cerevisiae and UniProt Accession Q12051

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EC Tree
IUBMB Comments
Some forms of this enzyme will also use geranyl diphosphate and dimethylallyl diphosphate as donors; it will not use larger prenyl diphosphates as efficient donors.
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This record set is specific for:
Saccharomyces cerevisiae
UNIPROT: Q12051
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Word Map
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
Synonyms
geranylgeranyl diphosphate synthase, ggpp synthase, ggdps, ggps1, ggpps1, cotb1, tgfpps, geranylgeranyl diphosphate synthase 1, geranylgeranyl pyrophosphate synthetase, ggppase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
farnesyltransferase
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geranylgeranyl diphosphate synthase
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geranylgeranyl pyrophosphate synthase
geranylgeranyl pyrophosphate synthetase
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geranylgeranyl-PP synthetase
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GGPP synthase
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short-chain type-III GGPP
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synthetase, geranylgeranyl pyrophosphate
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type-III geranylgeranyl pyrophosphate synthase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
show the reaction diagram
reaction mechanism and residues involved in substrate specificity and product chain lengt determination, overview
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
alkenyl group transfer
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PATHWAY SOURCE
PATHWAYS
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-, -, -, -, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase
Some forms of this enzyme will also use geranyl diphosphate and dimethylallyl diphosphate as donors; it will not use larger prenyl diphosphates as efficient donors.
CAS REGISTRY NUMBER
COMMENTARY hide
9032-58-0
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + geranylgeranyl diphosphate
show the reaction diagram
(E,E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + geranylgeranyl diphosphate
show the reaction diagram
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-
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?
(E,E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + geranylgeranyl diphosphate
show the reaction diagram
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mutants L138A and H139A synthesize larger products
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?
trans,trans-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + geranylgeranyl diphosphate
show the reaction diagram
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product distribution of the wild-type and mutant enzymes, overview, mechanism of product chain length determination
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + geranylgeranyl diphosphate
show the reaction diagram
trans,trans-farnesyl diphosphate + isopentenyl diphosphate
diphosphate + geranylgeranyl diphosphate
show the reaction diagram
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
N-[methyl(4-phenylbutyl)]-3-aminopropyl-1-hydroxy-1,1-bisphosphonate
the bisphosphonate binds only to the GGPP product inhibitory site
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Triton X-100
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activating at 0.1%
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00061 - 0.0467
(2E,6E)-farnesyl diphosphate
0.0014 - 0.0044
(E,E)-farnesyl diphosphate
0.0003 - 0.048
isopentenyl diphosphate
0.0008 - 0.267
isopentenyl diphosphate
0.0004 - 0.0051
trans,trans-farnesyl diphosphate
additional information
additional information
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kinetics of wild-type and mutant enzymes
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00013 - 0.11
(2E,6E)-farnesyl diphosphate
0.000042 - 0.025
(E,E)-farnesyl diphosphate
0.00013 - 0.11
isopentenyl diphosphate
1.6 - 8.4
trans,trans-farnesyl diphosphate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
biosynthesis of sclareol from geranylgeranyl diphosphate, overview
physiological function
GGPP synthase catalyzes all three isopentenyl diphosphate additions to dimethylally diphosphate, carrying out in the same active site the reactions catalyzed by both Erg20p (farnesyl diphosphate synthase, EC 2.5.1.10) and Bts1p (geranylgeranyl diphosphate synthase, EC 2.5.1.29)
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
44790
recombinant mutant H139A/R140A, gel filtration
47820
recombinant monomeric mutant M111E, gel filtration
72070
recombinant mutant N101A/Y105A, gel filtration
74740
recombinant mutant Y105A, gel filtration
75950
recombinant mutant N101A, gel filtration
76730
recombinant mutant N104A/Y105A, gel filtration
76990
recombinant mutant R140A, gel filtration
78690
recombinant mutant H139A, gel filtration
80350
recombinant mutant N104A, gel filtration
82300
recombinant wild-type enzyme, gel filtration
83880
recombinant mutant N101A/N104A/Y105A, gel filtration
84980
recombinant mutant N101A/N104A, gel filtration
85920
recombinant dimeric mutant M111E, gel filtration
88080
recombinant mutant M111F, gel filtration
92340
recombinant mutant M111A, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
dimerization is required for GGPPS activity, resdieus N101 and Y105 form H-bonds with H139 and R140 in the other subunit, and the H-bonds, mainly through N101 for maintaining substrate binding stability and the hydrophobic interaction of M111 in dimer interface, are essential for activity of yeast GGPPS
additional information
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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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop method, X-ray crystallographic structures of the N-[methyl(4-phenylbutyl)]-3-aminopropyl-1-hydroxy-1,1-bisphosphonate, bound to geranylgeranyl diphosphate synthase
structures of enzyme-inhibitor complexes with isopentenyl diphosphate, geranyl diphosphate, farnesyl diphosphate, geranylgeranyl diphosphate, zoledronate, minodronate, BPH-629, BPH-364, and BPH-675
the 3D structure of GGPPS reveals an unique positioning of the N-terminal helix A, which protrudes into the other subunit and stabilizes dimerization, although it is far from the main dimer interface. The replacement of residues L8 and I9 at this helix with Gly is sufficient to disrupt the dimer into a monomer, leading to at least 1000fold reduction in activity
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
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
DELTA 1-17
complete loss of activity, monomer
DELTA1-6
72% of wild-type activity. Dimer formation
DELTA1-7
29% of wild-type activity. Dimer and monomer formation
Delta1-8
0.3% of wild-type activity. Monomer formation
DELTA1-9
0.2% of wild-type activity. Monomer formation
E7G
84% of wild-type activity. Dimer and monomer formation
E7G/L8G
0.6% of wild-type activity
F96C
site-directed mutagenesis, the mutant shows increased sclareol biosynthesis compared to the wild-type
F96S
site-directed mutagenesis, the mutant shows increased sclareol biosynthesis compared to the wild-type
H139A
site-directed mutagenesis, the dimeric mutant shows altered kinetics compared to the wild-type enzyme
H139A/R140A
site-directed mutagenesis, inactive monomeric mutant
I9G
2.5% of wild-type activity
L8G
20% of wild-type activity. Dimer formation
L8G/I9G
0.3% of wild-type activity. Monomer formation
M111A
site-directed mutagenesis, the dimeric mutant shows altered kinetics compared to the wild-type enzyme
M111E
site-directed mutagenesis, the dimeric/monomeric mutant shows altered kinetics compared to the wild-type enzyme
M111F
site-directed mutagenesis, the dimeric mutant shows altered kinetics compared to the wild-type enzyme
N101A
site-directed mutagenesis, the dimeric mutant shows altered kinetics compared to the wild-type enzyme
N101A/N104A
site-directed mutagenesis, the dimeric mutant shows reduced kcat compared to the wild-type
N101A/N104A/Y105A
site-directed mutagenesis, inactive dimeric mutant
N101A/Y105A
site-directed mutagenesis, the dimeric mutant shows reduced kcat compared to the wild-type
N104A
site-directed mutagenesis, the dimeric mutant shows altered kinetics compared to the wild-type enzyme
N104A/Y105A
site-directed mutagenesis, the dimeric mutant shows slightly reduced activity compared to the wild-type
R140A
site-directed mutagenesis, the dimeric mutant shows altered kinetics compared to the wild-type enzyme
Y105A
site-directed mutagenesis, the dimeric mutant shows altered kinetics compared to the wild-type enzyme
Y95A
site-directed mutagenesis, the mutant shows increased sclareol biosynthesis compared to the wild-type
Y95C/F96H
site-directed mutagenesis, the mutant shows increased sclareol biosynthesis compared to the wild-type
Y95L/F96I
site-directed mutagenesis, the mutant shows increased sclareol biosynthesis compared to the wild-type
Y95S/F96H
site-directed mutagenesis, the mutant shows increased sclareol biosynthesis compared to the wild-type
F108A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
F108A/H139A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
H139A
L135A/H139A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
L138A
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mutation upstream from the G(Q/E) motif. Mutant forms larger condensation products than wild-type. With farnesyl diphosphate as allylic substrate, mutant produces large amounts of a C25 product
R140A
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no enzymic activity
S71Y
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
Y107A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
Y107A/F108A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
Y107A/F108A//L135A/H139A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
Y107A/F108A/H139A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
Y107A/H139A
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site-directed mutagenesis, mutant activity, substrate specificity, and product distribution compared to the wild-type enzyme
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes by nickel affinity chromatography from Escherichia coli strain JM109, removal of the tag by cleavage with Factor Xa
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene erg20 mutants, recombinant expression of N-terminally myc-tagged enzyme, coexpression of the enzyme fused to Cistus creticus 8-hydroxycopalyl diphosphate synthase, CcCLS in Saccharomyces cerevisiae strain AM205
gene GGPPS, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain JM109
expression of wild-type and mutant enzymes in Escheichia coli strain BL21(DE3)
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overexpression of geranylgeranyl pyrophosphate synthase from Saccharomyces cerevisiae (the BTS1 gene product) increases the intracellular beta-carotene levels due to the accelerated conversion of farnesyl pyrophosphate to geranylgeranyl diphosphate. Expression of BTS1 in Sacharomyces cerevisiae under the control of a strong and constitutive ADH1 promoter, leads to a 22fold increase in beta-carotene production
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
J. Biol. Chem.
281
14991-15000
2006
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Guo, R.T.; Cao, R.; Liang, P.H.; Ko, T.P.; Chang, T.H.; Hudock, M.P.; Jeng, W.Y.; Chen, C.K.; Zhang, Y.; Song, Y.; Kuo, C.J.; Yin, F.; Oldfield, E.; Wang, A.H.
Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases
Proc. Natl. Acad. Sci. USA
104
10022-10027
2007
Saccharomyces cerevisiae (Q12051)
Manually annotated by BRENDA team
Cao, R.; Chen, C.K.; Guo, R.T.; Wang, A.H.; Oldfield, E.
Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases
Proteins
73
431-439
2008
Saccharomyces cerevisiae (Q12051), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Lo, C.H.; Chang, Y.H.; Wright, J.D.; Chen, S.H.; Kan, D.; Lim, C.; Liang, P.H.
Combined experimental and theoretical study of long-range interactions modulating dimerization and activity of yeast geranylgeranyl diphosphate synthase
J. Am. Chem. Soc.
131
4051-4062
2009
Saccharomyces cerevisiae (Q12051), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Noike, M.; Katagiri, T.; Nakayama, T.; Nishino, T.; Hemmi, H.
Effect of mutagenesis at the region upstream from the G(Q/E) motif of three types of geranylgeranyl diphosphate synthase on product chain-length
J. Biosci. Bioeng.
107
235-239
2009
Saccharomyces cerevisiae, Pantoea ananatis, Sulfolobus acidocaldarius
Manually annotated by BRENDA team
Chang, C.K.; Teng, K.H.; Lin, S.W.; Chang, T.H.; Liang, P.H.
Control activity of yeast geranylgeranyl diphosphate synthase from dimer interface through H-bonds and hydrophobic interaction
Biochemistry
52
2783-2792
2013
Saccharomyces cerevisiae (Q12051), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Ignea, C.; Trikka, F.A.; Nikolaidis, A.K.; Georgantea, P.; Ioannou, E.; Loupassaki, S.; Kefalas, P.; Kanellis, A.K.; Roussis, V.; Makris, A.M.; Kampranis, S.C.
Efficient diterpene production in yeast by engineering Erg20p into a geranylgeranyl diphosphate synthase
Metab. Eng.
27
65-75
2015
Saccharomyces cerevisiae (Q12051), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Ukibe, K.; Hashida, K.; Yoshida, N.; Takagi, H.
Metabolic engineering of Saccharomyces cerevisiae for astaxanthin production and oxidative stress tolerance
Appl. Environ. Microbiol.
75
7205-7211
2009
Saccharomyces cerevisiae, Saccharomyces cerevisiae INVSc1
Manually annotated by BRENDA team