BRENDA - Enzyme Database
show all sequences of 4.1.99.16

Structural studies of geosmin synthase, a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence

Harris, G.G.; Lombardi, P.M.; Pemberton, T.A.; Matsui, T.; Weiss, T.M.; Cole, K.E.; Koeksal, M.; Murphy, F.V.; Vedula, L.S.; Chou, W.K.; Cane, D.E.; Christianson, D.W.; Biochemistry 54, 7142-7155 (2015)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
gene cyc2, recombinant expression of C-terminally His6-tagged full-length enzyme and of the N-terminal domain of ScGS (residues 1-366) in Escherichia coli strain BL21(DE3)pLysS , subcloning in Escherichia coli strain XL-1 Blue
Streptomyces coelicolor
Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified recombinant N-terminal domain of ScGS, unliganded and in complex with 3 Mg2+ ions and alendronate, mixing of 600 nl of 7 mg/ml protein in 25 mM Tris, pH 8.2, 5 mM MgCl2, 10 mM BME, and 1.5 mM sodium alendronate, with 600 nl of precipitant solution containing 0.2 M sodium acetate trihydrate, pH 7.0, and 20% w/v PEG 3350, and equilibration against 0.1 ml of reservoir solution at room temperature, X-ray diffraction structure determination and analysis at 2.4 A resolution. Neither full-length ScGS nor constructs of the C-terminal domain can be crystallized, but homology models of the C-terminal domain are constructed based on about 36% sequence identity with the N-terminal domain
Streptomyces coelicolor
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
each enzyme domain requires Mg2+ for catalysis, binding structure analysis at the N-terminal domain, overview
Streptomyces coelicolor
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
Streptomyces coelicolor
-
(-)-geosmin + acetone
-
-
?
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
-
(-)-geosmin + acetone
-
-
?
additional information
Streptomyces coelicolor
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
?
-
-
-
additional information
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
?
-
-
-
Organism
Organism
UniProt
Commentary
Textmining
Streptomyces coelicolor
Q9X839
-
-
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
Q9X839
-
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant C-terminally His6-tagged full-length enzyme from Escherichia coli strain BL21(DE3)pLysS by nickel affinity chromatography, recombinant N-terminal domain of ScGS (residues 1-366) from Escherichia coli strain BL21(DE3)pLysS by ammonium sulfate fractionation, adsorption chromatography on methyl resin, gel filtration, and ultrafiltartion
Streptomyces coelicolor
Reaction
Reaction
Commentary
Organism
Reaction ID
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O = (-)-geosmin + acetone
the active site in the N-terminal domain of enzyme ScGS catalyzes the ionization-dependent cyclization of FPP to form diphosphate and two cyclic products: germacradienol (major product, 85%) and germacrene D (minor product, 15%). After dissociation from the N-terminal domain, germacradienol is rebound to the active site of the C-terminal domain where it is converted to geosmin in a protonation-dependent cyclization reaction accompanied by the elimination of acetone through a retro-Prins reaction. The tandem cyclization-fragmentation reactions catalyzed by ScGS require two distinct active sites, a unique alphaalpha domain architecture is predicted for ScGS based on primary structure analysis
Streptomyces coelicolor
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
-
747096
Streptomyces coelicolor
(-)-geosmin + acetone
-
-
-
?
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
-
747096
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
(-)-geosmin + acetone
-
-
-
?
additional information
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
747096
Streptomyces coelicolor
?
-
-
-
-
additional information
geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. The enzyme has an alpha,alpha domain architecture, each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. There is no direct channel for transfer of the intermediate from the active site of the N-terminal domain to that of the C-terminal domain. It is a diiffusive transfer of the germacradienol intermediate
747096
Streptomyces coelicolor
?
-
-
-
-
additional information
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
747096
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
?
-
-
-
-
additional information
geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. The enzyme has an alpha,alpha domain architecture, each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. There is no direct channel for transfer of the intermediate from the active site of the N-terminal domain to that of the C-terminal domain. It is a diiffusive transfer of the germacradienol intermediate
747096
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
More
geosmin synthase has alpha-alpha domain architecture. The N-terminal domain and the C-terminal domain are separated by a 41-residue linker and share 28% and 29% amino acid sequence identity, respectively, with pentalenene synthase. Each domain contains characteristic metal ion-binding motifs of class I terpenoid cyclases. The aspartate-rich motif is found as D86DHFLE91 and D455DYYP459, and the NSE/DTE motif is found as N229DLFSYQRE237 and N598DVFSYQKE606. The C-terminal domain is also predicted to adopt an alpha fold homologous to that of the N-terminal domain based on approximately 36% amino acid sequence identity between these domains. Primary, secondary and quarternary enzyme structrue analysis, and homology modeling, overview
Streptomyces coelicolor
Synonyms
Synonyms
Commentary
Organism
Cyc2
-
Streptomyces coelicolor
ScGS
-
Streptomyces coelicolor
Cloned(Commentary) (protein specific)
Commentary
Organism
gene cyc2, recombinant expression of C-terminally His6-tagged full-length enzyme and of the N-terminal domain of ScGS (residues 1-366) in Escherichia coli strain BL21(DE3)pLysS , subcloning in Escherichia coli strain XL-1 Blue
Streptomyces coelicolor
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant N-terminal domain of ScGS, unliganded and in complex with 3 Mg2+ ions and alendronate, mixing of 600 nl of 7 mg/ml protein in 25 mM Tris, pH 8.2, 5 mM MgCl2, 10 mM BME, and 1.5 mM sodium alendronate, with 600 nl of precipitant solution containing 0.2 M sodium acetate trihydrate, pH 7.0, and 20% w/v PEG 3350, and equilibration against 0.1 ml of reservoir solution at room temperature, X-ray diffraction structure determination and analysis at 2.4 A resolution. Neither full-length ScGS nor constructs of the C-terminal domain can be crystallized, but homology models of the C-terminal domain are constructed based on about 36% sequence identity with the N-terminal domain
Streptomyces coelicolor
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
each enzyme domain requires Mg2+ for catalysis, binding structure analysis at the N-terminal domain, overview
Streptomyces coelicolor
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
Streptomyces coelicolor
-
(-)-geosmin + acetone
-
-
?
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
-
(-)-geosmin + acetone
-
-
?
additional information
Streptomyces coelicolor
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
?
-
-
-
additional information
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
?
-
-
-
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant C-terminally His6-tagged full-length enzyme from Escherichia coli strain BL21(DE3)pLysS by nickel affinity chromatography, recombinant N-terminal domain of ScGS (residues 1-366) from Escherichia coli strain BL21(DE3)pLysS by ammonium sulfate fractionation, adsorption chromatography on methyl resin, gel filtration, and ultrafiltartion
Streptomyces coelicolor
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
-
747096
Streptomyces coelicolor
(-)-geosmin + acetone
-
-
-
?
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O
-
747096
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
(-)-geosmin + acetone
-
-
-
?
additional information
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
747096
Streptomyces coelicolor
?
-
-
-
-
additional information
geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. The enzyme has an alpha,alpha domain architecture, each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. There is no direct channel for transfer of the intermediate from the active site of the N-terminal domain to that of the C-terminal domain. It is a diiffusive transfer of the germacradienol intermediate
747096
Streptomyces coelicolor
?
-
-
-
-
additional information
geosmin synthase is a bifunctional sesquiterpene synthase with alpha-alpha domain architecture that catalyzes a unique cyclization fragmentation reaction sequence
747096
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
?
-
-
-
-
additional information
geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. The enzyme has an alpha,alpha domain architecture, each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. There is no direct channel for transfer of the intermediate from the active site of the N-terminal domain to that of the C-terminal domain. It is a diiffusive transfer of the germacradienol intermediate
747096
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
More
geosmin synthase has alpha-alpha domain architecture. The N-terminal domain and the C-terminal domain are separated by a 41-residue linker and share 28% and 29% amino acid sequence identity, respectively, with pentalenene synthase. Each domain contains characteristic metal ion-binding motifs of class I terpenoid cyclases. The aspartate-rich motif is found as D86DHFLE91 and D455DYYP459, and the NSE/DTE motif is found as N229DLFSYQRE237 and N598DVFSYQKE606. The C-terminal domain is also predicted to adopt an alpha fold homologous to that of the N-terminal domain based on approximately 36% amino acid sequence identity between these domains. Primary, secondary and quarternary enzyme structrue analysis, and homology modeling, overview
Streptomyces coelicolor
General Information
General Information
Commentary
Organism
additional information
neither full-length ScGS nor constructs of the C-terminal domain can be crystallized, but homology models of the C-terminal domain are constructed based on about 36% sequence identity with the N-terminal domain, analysis of the crystal structure of the N-terminal domain in unliganded or liganded form, overview. Possible alpha,alpha domain architectures as frameworks for bifunctional catalysis
Streptomyces coelicolor
physiological function
geosmin is a powerful odorant with an extremely low human detection threshold of less than 10 parts-per-trillion, and is mainly responsible for the characteristic odor of freshly turned earth. Although geosmin contributes to the pleasant, earthy flavor of beets, it is also a commonly occurring contaminant of musty-tasting water, wine, and fish. Geosmin is not known to cause human disease, but its detection and elimination from potable water sources is a critical environmental and water quality issue
Streptomyces coelicolor
General Information (protein specific)
General Information
Commentary
Organism
additional information
neither full-length ScGS nor constructs of the C-terminal domain can be crystallized, but homology models of the C-terminal domain are constructed based on about 36% sequence identity with the N-terminal domain, analysis of the crystal structure of the N-terminal domain in unliganded or liganded form, overview. Possible alpha,alpha domain architectures as frameworks for bifunctional catalysis
Streptomyces coelicolor
physiological function
geosmin is a powerful odorant with an extremely low human detection threshold of less than 10 parts-per-trillion, and is mainly responsible for the characteristic odor of freshly turned earth. Although geosmin contributes to the pleasant, earthy flavor of beets, it is also a commonly occurring contaminant of musty-tasting water, wine, and fish. Geosmin is not known to cause human disease, but its detection and elimination from potable water sources is a critical environmental and water quality issue
Streptomyces coelicolor
Other publictions for EC 4.1.99.16
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
743387
Schifrin
A single terpene synthase is ...
Sorangium cellulosum, Sorangium cellulosum Soce56
Org. Biomol. Chem.
14
3385-3393
2016
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2
2
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747096
Harris
Structural studies of geosmin ...
Streptomyces coelicolor, Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
Biochemistry
54
7142-7155
2015
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1
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2
2
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747590
Zhou
-
Cloning and expression analys ...
Aphanizomenon gracile, Aphanizomenon gracile WH-1
Chin. J. Appl. Environ. Biol.
21
824-829
2015
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1
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728186
Giglio
Expression of the geosmin synt ...
Dolichospermum circinale, Dolichospermum circinale AWQC318
J. Phycol.
47
1338-1343
2011
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1
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712642
Singh
Exploration of geosmin synthas ...
Streptomyces peucetius, Streptomyces peucetius ATCC 27952
J. Ind. Microbiol. Biotechnol.
36
1257-1265
2009
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6
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692761
Jiang
Geosmin biosynthesis. Mechanis ...
Streptomyces coelicolor
J. Am. Chem. Soc.
130
428-429
2008
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680396
Cane
Geosmin biosynthesis in Strept ...
Streptomyces avermitilis
J. Antibiot.
59
471-479
2006
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7
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