Information on EC 4.2.3.75 - (-)-germacrene D synthase

New: Word Map on EC 4.2.3.75
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Mark a special word or phrase in this record:
Search Reference ID:
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


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

EC NUMBER
COMMENTARY hide
4.2.3.75
-
RECOMMENDED NAME
GeneOntology No.
(-)-germacrene D synthase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate = (-)-germacrene D + diphosphate
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
germacrene biosynthesis
-
-
Sesquiterpenoid and triterpenoid biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate diphosphate-lyase [(-)-germacrene-D-forming]
In Solidago canadensis the biosynthesis results in the pro-R hydrogen at C-1 of the farnesy diphosphate ending up at C-11 of the (-)-germacrene D [1]. With Streptomyces coelicolor the pro-S hydrogen at C-1 ends up at C-11 of the (-)-germacrene D [2].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
bifunctional germacradienol/germacrene D synthase
-
-
Manually annotated by BRENDA team
bifunctional germacradienol/germacrene D synthase
-
-
Manually annotated by BRENDA team
; cv. Chardonnay and cv. Gewürztraminer
SwissProt
Manually annotated by BRENDA team
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
(-)-germacrene D + diphosphate
show the reaction diagram
2-trans,6-trans-farnesyl diphosphate
(-)-(7S)-germacrene D + diphosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2-trans,6-trans-farnesyl diphosphate
(-)-(7S)-germacrene D + diphosphate
show the reaction diagram
Q6Q3H3
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
replacement of Mg2+ by Mn2+ results in loss of product beta-copaene. Presence of K+ decreases the (?)-germacrene D yield and instead increases the overall yield of tricyclic sesquiterpene olefins
Mn2+
-
replacement of Mg2+ by Mn2+ results in loss of product beta-copaene. In the presence of the Mn2+, Cop4 favors a reaction path that ends after one cyclization in (?)-germacrene D
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0029 - 0.011
(2E,6E)-farnesyl diphosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.012 - 0.03
(2E,6E)-farnesyl diphosphate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1 - 10.3
(2E,6E)-farnesyl diphosphate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
at pH 5.0 cyclization can proceed via a 1,6 ring closure to also yield a small amount of delta-cadinene, 12% of total sesquiterpene products, in addition to (?)-germacrene D
10
-
at pH 10, the cyclization reaction ends with the hydride shift and deprotonation of the germacradienyl cation to yield (?)-germacrene D, 91% of total sesquiterpene products
additional information
-
under both alkaline and acidic conditions Cop4 becomes a very selective enzyme with only one major product (?)-germacrene D compared to three major compounds produced under neutral reaction conditions. At pH 10, the cyclization reaction ends with the hydride shift and deprotonation of the germacradienyl cation to yield (?)-germacrene D, 91% of total sesquiterpene products, while at pH 5.0 cyclization can proceed via a 1,6 ring closure to also yield a small amount of delta-cadinene, 12% of total sesquiterpene products, in addition to (?)-germacrene D
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
the catalytic fidelity of Cop4 can be drastically altered by varying reactions conditions
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 25
-
lowering the reaction temperature from 25°C to 4°C increases the selectivity of Cop4 for (?)-germacrene D and decreases the fraction of structurally unidentified sesquiterpene olefins by half
37
-
increasing the reaction temperature to 37°C decreases the fidelity of Cop4. At 37°C Cop4 generates a relative larger fraction of products beta-cubebene, sativene, delta-cadinene and beta-copaene that are derived from a cadinyl cation intermediate
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5
calculated
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
; strongest hybridization signals with RNA from flower budsand strongly reduced transcript levels in pre- and postanthesis open flowers and in set flowers at early fruit onset
Manually annotated by BRENDA team
additional information
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis of Vitis vinifera cv. Gewürztraminer, phylogenetic tree, expression in Escherichia coli strain BL21(DE3)-RIL; expression in Escherichia coli
expression in Escherichia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
transcript level of Tps1 in leaf is strongly induced by feeding forest tent caterpillars and follows diurnal rhythm
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D303E
less than 0.25% of wild-type activity
D303N
mimicking of corresponding amino acid in (+)-germacrene D synthase Sc11. 10% of the wild-type, activity, reduction in catalytic constant by a factor of 10, with no change in Km of farnesyl diphosphate, product composition or chirality