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Information on EC 4.2.3.22 - germacradienol synthase and Organism(s) Streptomyces coelicolor and UniProt Accession Q9X839
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4.2.3.22 germacradienol synthaseIUBMB Comments
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 . 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 . Also catalyses the reaction of EC 4.2.3.75, (-)-germacrene D synthase.
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The taxonomic range for the selected organisms is: Streptomyces coelicolor
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
Synonyms
terpene cyclase, germacrene d synthase, spterp13, germacradienol/geosmin synthase, germacradienol synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
reaction mechanism
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(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
catalytic mechanism via intermediate is (7R)-germacra-1(10),4-diene-11-ol
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
PATHWAY SOURCE
PATHWAYS
-
-
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.
CAS REGISTRY NUMBER
COMMENTARY
211049-88-6
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germa-1(10),5-dien-11-ol + diphosphate
-
catalysed by the N-terminal domain of the bifunctional enzyme
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
-
trans-1,10-dimethyl-trans-9-decalol
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
2-trans,6-trans-farnesyl diphosphate + H2O
(4S,7R)-germacra-1(10)E,5E-dien-11-ol + diphosphate
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
-
enzyme is essential for geosmin biosynthesis
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
-
enzyme is involved in geosmin biosynthesis
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
-
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
-
reaction is catalyzed by one of two sesquiterpene domains of the enzyme
-
-
?
2-trans,6-trans-farnesyl diphosphate + H2O
(4S,7R)-germacra-1(10)E,5E-dien-11-ol + diphosphate
-
key step in biosynthesis of geosmin
-
-
?
2-trans,6-trans-farnesyl diphosphate + H2O
(4S,7R)-germacra-1(10)E,5E-dien-11-ol + diphosphate
-
cyclization reaction, detailed mechanism, an intermediate is (7R)-germacra-1(10),4-diene-11-ol
GC-MS and NMR product configuration analysis
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?
additional information
?
-
-
no activity with geranylgeranyl diphosphate
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-
?
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
?
-
-
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 SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
2-trans,6-trans-farnesyl diphosphate + H2O
(4S,7R)-germacra-1(10)E,5E-dien-11-ol + diphosphate
-
key step in 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
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
-
enzyme is essential for geosmin biosynthesis
-
-
?
(2E,6E)-farnesyl diphosphate + H2O
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
-
enzyme is involved in geosmin biosynthesis
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
additional information
-
enzyme activity is dependent on divalent cations
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000062
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30°C, recombinant enzyme
0.000115
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30°C, recombinant N-terminal domain
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3.2
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30°C, recombinant N-terminal domain
6.2
2-trans,6-trans-farnesyl diphosphate
-
pH 8.2, 30°C, recombinant enzyme
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
construction of an ordered library of Supercos-1 clones, DNA sequence determination and analysis, subcloning in Escherichia coli
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
solubilization of recombinant enzyme from inclusion bodies by 0.02% Triton X-100 and 100 mM NaOH, and refolding
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
He, X.; Cane, D.E.
Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2)
J. Am. Chem. Soc.
126
2678-2679
2004
Streptomyces coelicolor, Streptomyces coelicolor A3(2)
Gust, B.; Challis, G.L.; Fowler, K.; Kieser, T.; Chater, K.F.
PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin
Proc. Natl. Acad. Sci. USA
100
1541-1546
2003
Streptomyces coelicolor
Cane, D.E.; Watt, R.M.
Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis
Proc. Natl. Acad. Sci. USA
100
1547-1551
2003
Streptomyces coelicolor, Streptomyces coelicolor A3(2)
Jiang, J.; He, X.; Cane, D.E.
Geosmin biosynthesis. Streptomyces coelicolor germacradienol/germacrene D synthase converts farnesyl diphosphate to geosmin
J. Am. Chem. Soc.
128
8128-8129
2006
Streptomyces coelicolor (Q9X839), Streptomyces coelicolor
Jiang, J.; Cane, D.E.
Geosmin biosynthesis. Mechanism of the fragmentation-rearrangement in the conversion of germacradienol to geosmin
J. Am. Chem. Soc.
130
428-429
2008
Streptomyces coelicolor
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