Information on EC 4.2.3.22 - germacradienol synthase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY
4.2.3.22
-
RECOMMENDED NAME
GeneOntology No.
germacradienol synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
-
-
-
-
(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
catalytic mechanism via intermediate is (7R)-germacra-1(10),4-diene-11-ol
-
(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
reaction mechanism
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
cyclization
Q82L49, -
-
additional information
-
germacradienol/geosmin synthase is a bifunctional enzyme in which the N-terminal domain of the protein converts farnesyl diphosphate, while the C-terminal domain catalyzes the transformation of germacradienol to geosmin
additional information
B0FLN6
putative function is as a germacradienol synthase/terpene cyclase
PATHWAY
KEGG Link
MetaCyc Link
Biosynthesis of secondary metabolites
-
geosmin biosynthesis
-
Metabolic pathways
-
Sesquiterpenoid and triterpenoid biosynthesis
-
SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]
Requires Mg2+ for activity. H-1si of farnesyl diphosphate is lost in the formation of (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol. Formation of (-)-germacrene D involves a stereospecific 1,3-hydride shift of H-1si of farnesyl diphosphate. Both products are formed from a common intermediate [2]. Other enzymes produce germacrene D as the sole product using a different mechanism. The enzyme mediates a key step in the biosynthesis of geosmin (see EC 4.1.99.16 geosmin synthase), a widely occurring metabolite of many streptomycetes, bacteria and fungi [2]. Also catalyses the reaction of EC 4.2.3.75, (-)-germacrene D synthase.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Cyc2
Q9X839
gene name
germacradienol synthase
-
-
germacradienol synthase
B0FLN6
-
germacradienol/geosmin synthase
-
-
germacradienol/germacrene D synthase
Q82L49
-
germacradienol/germacrene D synthase
Q9X839
-
germacradienol/germacrene D synthase
-
-
germacrene D synthase
Q49SP6
-
sesquiterpene synthase
-
-
sesquiterpene synthase
-
-
spterp13
B0FLN6
-
CAS REGISTRY NUMBER
COMMENTARY
211049-88-6
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
germacradienol/germacrene D synthase
UniProt
Manually annotated by BRENDA team
several strains, gene cyc2 or Sco6073 encoding an enzyme with two sesquiterpene synthase domains
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
Q49SP6
-
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
Q82L49, -
-
66%
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
Q9X839
-
trans-1,10-dimethyl-trans-9-decalol
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
-
enzyme is essential for geosmin biosynthesis
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
-
enzyme is involved in geosmin biosynthesis, cyclization reaction, mechanism of full length enzyme and N-terminal catalytic domain
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
-
reaction is catalyzed by one of two sesquiterpene domains of the enzyme
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
B0FLN6, -
Mg-dependent conversion
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germa-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
Q9X839
-
catalysed by the N-terminal domain of the bifunctional enzyme
-
?
2-trans,6-trans-farnesyl diphosphate + H2O
(4S,7R)-germacra-1(10)E,5E-dien-11-ol + diphosphate
show the reaction diagram
-
key step in biosynthesis of geosmin
-
-
?
2-trans,6-trans-farnesyl diphosphate + H2O
(4S,7R)-germacra-1(10)E,5E-dien-11-ol + diphosphate
show the reaction diagram
-
cyclization reaction, detailed mechanism, an intermediate is (7R)-germacra-1(10),4-diene-11-ol
GC-MS and NMR product configuration analysis
-
?
additional information
?
-
-
no activity with geranylgeranyl diphosphate
-
-
-
additional information
?
-
-
stereospecificity, the 1,3-hydride shift of the (-)-germacrene D synthase of Streptomyces coelicolor A3(2) is opposite to the enzyme from Solidago canadensis
-
-
-
additional information
?
-
B0FLN6, -
catalyze the Mg-dependent conversion of farnesyl diphosphate to the germacradienol, an essential step in the biosynthesis of geosmin
-
-
-
additional information
?
-
-
catalyzes the Mg2+-dependent cyclization of conversion of farnesyl diphosphate to a mixture of germacradienol, germacrene D, and geosmin, accompanied by small amounts of octalin
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
Q49SP6
-
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
-
enzyme is essential for geosmin biosynthesis
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
-
enzyme is involved in geosmin biosynthesis
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
show the reaction diagram
B0FLN6, -
Mg-dependent conversion
-
-
?
2-trans,6-trans-farnesyl diphosphate + H2O
(4S,7R)-germacra-1(10)E,5E-dien-11-ol + diphosphate
show the reaction diagram
-
key step in biosynthesis of geosmin
-
-
?
additional information
?
-
B0FLN6, -
catalyze the Mg-dependent conversion of farnesyl diphosphate to the germacradienol, an essential step in the biosynthesis of geosmin
-
-
-
additional information
?
-
-
catalyzes the Mg2+-dependent cyclization of conversion of farnesyl diphosphate to a mixture of germacradienol, germacrene D, and geosmin, accompanied by small amounts of octalin
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Co2+
-
can substitute for Mg2+
Co2+
Q82L49, -
10-20% activity, compared to reaction with Mg2+
Cu2+
-
can substitute for Mg2+
Cu2+
Q82L49, -
10-20% activity, compared to reaction with Mg2+
Fe2+
-
can substitute for Mg2+
Fe2+
Q82L49, -
50% activity, compared to reaction with Mg2+
Fe3+
-
can substitute for Mg2+
Mg2+
-
required, preferred divalent cation
Mg2+
Q82L49, -
100% activity
Mg2+
B0FLN6
10 mM are included in assay medium
Mn2+
-
can substitute for Mg2+
Ni2+
-
can substitute for Mg2+
Zn2+
-
can substitute for Mg2+
Zn2+
Q82L49, -
50% activity, compared to reaction with Mg2+
Mn2+
Q82L49, -
10-20% activity, compared to reaction with Mg2+
additional information
-
enzyme activity is dependent on divalent cations
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
Cu2+
Q9X839
suppresses the formation of geosmin by factor 3 or more
Fe2+
Q9X839
suppresses the formation of geosmin by factor 3 or more
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.000062
-
(2E,6E)-farnesyl diphosphate
Q9X839
pH 8.2, 30C
0.000062
-
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30C, recombinant enzyme
-
0.000115
-
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30C, recombinant N-terminal domain
-
0.000075
-
farnesyl diphosphate
Q82L49, -
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0062
-
(2E,6E)-farnesyl diphosphate
Q9X839
pH 8.2, 30C
3.2
-
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30C, recombinant N-terminal domain
-
6.2
-
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30C, recombinant enzyme
-
0.0031
-
farnesyl diphosphate
Q82L49, -
-
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
100
-
(2E,6E)-farnesyl diphosphate
Q9X839
pH 8.2, 30C
263972
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
-
Q49SP6
activity assay
8.2
-
Q82L49, -
activity assay
8.2
-
B0FLN6
assay at
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.6
9
Q82L49, -
-
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
Q49SP6
activity assay
30
-
Q9X839
activity assay
30
-
Q82L49, -
activity assay
30
-
B0FLN6
assay at
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
B0FLN6
strain ATCC 27952 produces clinically important anthracycline chemotherapeutic agents of the polyketide class of antibiotics, daunorubicin and doxorubicin
Manually annotated by BRENDA team
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
83000
-
Q82L49, -
determined by SDS-PAGE
98000
-
B0FLN6
recombinant Spterp13, consistent with the predicted mass of Spterp13 plus his-tag determined by SDS-PAGE analysis
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 40000, recombinant enzyme, SDS-PAGE
additional information
Q9X839
the recombinant N-terminal half of the protein catalyzes the Mg2+-dependent cyclization of farnesyl diphosphate to germacradienol and germacrene D, while the highly homologous C-terminal domain catalyzes the Mg2+-dependent conversion of germacradienol to geosmin
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
using Q-Sepharose resin and a Q-Sepharose column
Q82L49, -
recombinant enzyme from Escherichia coli strain BL21(DE3), soluble enzyme and enzyme solubilized and refolded from inclusion bodies, by ion exchange chromatography and gel filtration
-
purification by Co2+-affinity chromatography
B0FLN6
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
into the pCR2.1-TOPO vector, for functional expression full-length cDNA is sub-cloned into a pET vector
Q49SP6
for construction of a geoA-deletion mutant of Streptomyces avermitilis, and for expression in Escherichia coli BL21DE3 cells
Q82L49, -
construction of an ordered library of Supercos-1 clones, DNA sequence determination and analysis, subcloning in Escherichia coli
-
for expression in Escherichia coli
Q9X839
expression in Escherichia coli strain BL21(DE3)
-
full length recombinant protein is heterologously expressed as a his-tagged fusion protein in Escherichia coli
B0FLN6
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
construction of a cyc2 disruption mutant inactive in geosmin biosynthesis
additional information
-
expression of isolated N-terminal and C-terminal domains reveals that the N-terminal domain is responsible for the catalytic activity, while the C-terminal domain is barely active
Renatured/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
resuspended inclusion body protein is refolded
Q82L49, -
solubilization of recombinant enzyme from inclusion bodies by 0.02% Triton X-100 and 100 mM NaOH, and refolding
-