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Information on EC 1.13.12.19 - 2-oxoglutarate dioxygenase (ethene-forming)
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1.13.12.19 2-oxoglutarate dioxygenase (ethene-forming)IUBMB Comments
This is one of two simultaneous reactions catalysed by the enzyme, which is responsible for ethene production in bacteria of the Pseudomonas syringae group. In the other reaction [EC 1.14.20.7, 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)] the enzyme catalyses the mono-oxygenation of both 2-oxoglutarate and L-arginine, forming succinate, carbon dioxide and L-hydroxyarginine, which is subsequently cleaved into guanidine and (S)-1-pyrroline-5-carboxylate.The enzymes catalyse two cycles of the ethene-forming reaction for each cycle of the succinate-forming reaction, so that the stoichiometry of the products ethene and succinate is 2:1.
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Word Map
- 1.13.12.19
-
1-aminocyclopropane-1-carboxylic
-
2og-feii
- syringae
-
climacteric
- carnation
-
dianthus
-
photoautotrophic
- biotechnology
- agriculture
- synthesis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
ethylene forming enzyme, 2og-fe(ii) oxygenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2-oxoglutarate-Fe(II) oxygenase
2OG-Fe(II) oxygenase
EFE
ethylene forming enzyme
ethylene-forming enzyme
additional information
ethylene-forming enzyme
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
-
-
-
-
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
reaction mechanism, overview
-
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
reaction mechanism, overview
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
reaction mechanism, overview
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
reaction mechanism, overview
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
mechanism of ethylene formation, and two-pathway reaction mechanism of EFE, structure-function relationship
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
Pseudomonas syringae ethylene-forming enzyme reveal a branched mechanism. In one branch, an apparently typical 2-oxoglutarate oxygenase reaction to give succinate, carbon dioxide, and sometimes pyrroline-5-carboxylate occurs, reaction of EC 1.13.11.34. Alternatively, Grob-type oxidative fragmentation of a 2-oxoglutarate-derived intermediate occurs to give ethylene and carbon dioxide, EC 1.13.12.19. Fragmentation to give ethylene is promoted by binding of L-arginine in a nonoxidized conformation and of 2-oxoglutarate in an unprecedented high-energy conformation that favors ethylene, relative to succinate formation. Induced fit reaction mechanism, detailed overview
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
mechanism of ethylene formation, and two-pathway reaction mechanism of EFE, structure-function relationship
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-
2-oxoglutarate + O2 = ethene + 3 CO2 + H2O
reaction mechanism, overview
-
-
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PATHWAY SOURCE
PATHWAYS
-
, ,
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SYSTEMATIC NAME
IUBMB Comments
2-oxoglutarate:oxygen oxidoreductase (decarboxylating, ethene-forming)
This is one of two simultaneous reactions catalysed by the enzyme, which is responsible for ethene production in bacteria of the Pseudomonas syringae group. In the other reaction [EC 1.14.20.7, 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)] the enzyme catalyses the mono-oxygenation of both 2-oxoglutarate and L-arginine, forming succinate, carbon dioxide and L-hydroxyarginine, which is subsequently cleaved into guanidine and (S)-1-pyrroline-5-carboxylate.The enzymes catalyse two cycles of the ethene-forming reaction for each cycle of the succinate-forming reaction, so that the stoichiometry of the products ethene and succinate is 2:1.
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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
2-oxoglutarate + O2
ethylene + ?
presence of oxygen is essential for the ethylene forming reaction by EFE
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
2-oxoglutarate + O2
ethene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethene + 3 CO2 + H2O
in the other reaction [EC 1.14.20.7, 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)] the enzyme catalyses the mono-oxygenation of both 2-oxoglutarate and L-arginine, forming succinate, carbon dioxide and L-hydroxyarginine, which is subsequently cleaved into guanidine and (S)-1-pyrroline-5-carboxylate. An iron(IV)-oxo intermediate initiates L-arginine oxidation but not ethylene production by the 2-oxoglutarate-dependent oxygenase, ethylene-forming enzyme
-
-
?
2-oxoglutarate + O2
ethene + 3 CO2 + H2O
in the other reaction [EC 1.14.20.7, 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)] the enzyme catalyses the mono-oxygenation of both 2-oxoglutarate and L-arginine, forming succinate, carbon dioxide and L-hydroxyarginine, which is subsequently cleaved into guanidine and (S)-1-pyrroline-5-carboxylate. The reaction mechanism of the enzyme (EFE) is studied with QM/MM methods. Based on the results, a branched pathway for the enzyme that can lead either to ethylene or to succinate via L-Arg hydroxylation is proposed. After formation of the Fe-O2 species, the nucleophilic attack of distal oxygen on the keto carbon of 2-oxoglutarate is accompanied by the breaking of the C1-C2 bond in 2-oxoglutarate, leading to an FeII-peroxysuccinate complex with a dissociated CO2. This FeII-peroxysuccinate species serves as the branch point intermediate in the dual transformations by EFE. It can proceed in two directions. In one branch, the subsequent O-O bond cleavage generates the succinate-bound FeIV-oxo intermediate. Next a nearby water molecule binds to the iron to form a hexacoordinated FeIV-oxo intermediate. Hydrogen atom abstraction from L-Arg, hydroxyl radical rebound, and elimination of guanidine from the hydroxylated L-Arg product complete the cycle. This represents the well-established mechanism for substrate oxidation by Fe/2OG oxygenases. Alternatively, starting from FeII-peroxysuccinate, the CO2 insertion into the Fe-O bond gives a peroxic anhydride species. Further steps, including the water binding, O-O bond cleavage, intermolecular proton transfer, and two consecutive C-C bond breaking steps, result in the formation of ethylene. According to the proposed reaction mechanism of EFE, a competition between the CO2 insertion and the O-O bond cleavage from the branch point intermediate governs the product selectivity. The calculated reaction barriers show a preference for the CO2 insertion reaction
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
ethylene forming reaction
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
the enzyme is dependent on 2-oxoglutarate
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
ethylene forming reaction
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
enzyme is highly specific for substrate 2-oxoglutarate
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
-
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34, reaction, mechanism of the two reaction catalyzed at the same time, overview. Enzyme EFE converts 2-oxoglutarate into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of L-arginine driven by the oxidative decarboxylation of 2-oxoglutarate to form succinate and CO2
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34, reaction, mechanism of the two reaction catalyzed at the same time, overview. Enzyme EFE converts 2-oxoglutarate into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of L-arginine driven by the oxidative decarboxylation of 2-oxoglutarate to form succinate and CO2
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
-
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
additional information
?
-
cf. EC 1.14.11.34, reaction via 5-hydroxyarginine. Selected L-Arg derivatives induce ethylene formation without undergoing hydroxylation, demonstrating that ethylene production and L-Arg hydroxylation activities are not linked. Enzyme EFE utilizes the alternative 2-oxo acid 2-oxoadipate as a cosubstrate (forming glutaric acid) during the hydroxylation of L-Arg, with this reaction unlinked from ethylene formation. The amount of ethylene produced is more than twice the levels of succinate, L-DELTA1-pyrroline-5-carboxylate, or guanidine generated
-
-
?
additional information
?
-
Pseudomonas syringae ethylene-forming enzyme reveal a branched mechanism. In one branch, an apparently typical 2-oxoglutarate oxygenase reaction to give succinate, carbon dioxide, and sometimes pyrroline-5-carboxylate occurs, reaction of EC 1.13.11.34. Alternatively, Grob-type oxidative fragmentation of a 2-oxoglutarate-derived intermediate occurs to give ethylene and carbon dioxide, EC 1.13.12.19. Fragmentation to give ethylene is promoted by binding of L-arginine in a nonoxidized conformation and of 2-oxoglutarate in an unprecedented high-energy conformation that favors ethylene, relative to succinate formation. Role for Tyr192 in catalysis, substrate binding structures, structure-function analysis, overview
-
-
?
additional information
?
-
substrate binding structures, crystal structure analysis, overview. In all cases of bound 2-oxoglutarate, the carboxylate distal to the metal is stabilized by a salt bridge with R277, and the carboxylate coordinating the metal is stabilized by hydrogen bonds with R171. The C1-carboxylate oxygen of 2-oxoglutarate binds approximately trans to the distal H268 and the C2-oxo oxygen binds opposite D191. L-Arg binds near, but does not coordinate, the metal center in EFE-Mn-2OG-L-Arg
-
-
?
additional information
?
-
cf. EC 1.14.11.34, reaction via 5-hydroxyarginine. Selected L-Arg derivatives induce ethylene formation without undergoing hydroxylation, demonstrating that ethylene production and L-Arg hydroxylation activities are not linked. Enzyme EFE utilizes the alternative 2-oxo acid 2-oxoadipate as a cosubstrate (forming glutaric acid) during the hydroxylation of L-Arg, with this reaction unlinked from ethylene formation. The amount of ethylene produced is more than twice the levels of succinate, L-DELTA1-pyrroline-5-carboxylate, or guanidine generated
-
-
?
additional information
?
-
substrate binding structures, crystal structure analysis, overview. In all cases of bound 2-oxoglutarate, the carboxylate distal to the metal is stabilized by a salt bridge with R277, and the carboxylate coordinating the metal is stabilized by hydrogen bonds with R171. The C1-carboxylate oxygen of 2-oxoglutarate binds approximately trans to the distal H268 and the C2-oxo oxygen binds opposite D191. L-Arg binds near, but does not coordinate, the metal center in EFE-Mn-2OG-L-Arg
-
-
?
additional information
?
-
enzyme catalyzes the formation of ethylene and succinate from 2-oxoglutarate, at a molar ratio of 2:l, reactions of EC 1.13.12.19 and EC 1.14.11.34. In the main reaction, 2-oxoglutarate is dioxygenated to produce one molecule of ethylene and three molecules of carbon dioxide. In the sub-reaction, both 2-oxoglutarate and L-arginine are mono-oxygenated to yield succinate plus carbon dioxide and L-hydroxyarginine, respectively, the latter being further transformed to guanidine and L-delta-pyrroline-5-carboxylate. Dual-circuit mechanism for the entire reaction is proposed, in which the binding of L-arginine and 2-oxoglutarate in a Schiff-base structure generates a common intermediate for two reactions
-
-
?
additional information
?
-
presence of 2-oxoglutarate, L-arginine, Fe2+ and oxygen is essential for the enzymic reaction
-
-
?
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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
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
2-oxoglutarate + O2
ethene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
2-oxoglutarate + O2
ethylene + 3 CO2 + H2O
-
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
-
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
-
cf. EC 1.14.11.34
-
-
?
3 2-oxoglutarate + L-arginine + 3 O2
2 C2H4 + succinate + 7 CO2 + 3 H2O + guanidine + L-DELTA1-pyrroline-5-carboxylate
cf. EC 1.14.11.34
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Fe2+
dependent on, required for catalysis
Fe2+
dependent on, required for catalysis. The overall metal-binding mode of PsEFE is relatively typical for 2OG oxygenases, with the metal coordinated by His189 (C terminus of DSBH II), Asp191 (loop linking DSBH II and III), and His268 (N-terminus of DSBH VII)
Fe2+
dependent on, residues H189, D191 and H268 are responsible for binding the Fe(II) ligand
Fe2+
non-heme Fe(II)-dependent ethylene-forming enzyme, the metal ion is hexa-coordinated
Fe2+
at the active site, enzyme acts as a bidentate ligand and it forms a complex with Fe2+. The Fe2+ is further coordinated to a tridentate Schiff base of 2-oxoglutarate and L-arginine, whose terminal carboxylate and guanidino groups are trapped by binding sites I and II on the enzyme, respectively
Fe2+
-
the nonheme iron(II) oxygenase catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinate and CO2 to generate a highly reactive iron species that hydroxylates a specific alkane C-H bond, in this case targeting L-arginine (Arg) for hydroxylation
Fe2+
dependent on, residues H189, D191 and H268 are responsible for binding the Fe(II) ligand
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4,5-dihydroxy-1,3-benzene disulfonic acid
1 mM, 0.8% residual activity
N-oxalylglycine
an unreactive 2-oxoglutarate analogue, enzyme binding structure analysis, overview
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
L-arginine
highly specific for cofactor L-arginine, KM value 0.018 mM
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 9
over 50% of maximal activity within this range
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
brenda
gene is encoded by an indigenous plasmid, designated pPSP1; pv. phaseolicola PK2
UniProt
brenda
pv. phaseolicola PK2, enzyme catalyzes the formation of ethylene and succinate from 2-oxoglutarate, reactions of EC 1.13.12.19 and EC 1.14.11.34
UniProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
additional information
evolution
emzyme PsEFE should be regarded as a hybrid of subgroups I and II, in terms of its classification
evolution
enzyme EFE is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. It contains a double-stranded beta-helix (DSBH, also known as the jellyroll or cupin fold) core typically found in members of the Fe(II)/2OG-dependent oxygenases
evolution
ethylene-forming enzyme (EFE) is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily
evolution
the enzyme belongs to a subclass of 2-oxoglutarate/Fe(II) dependent dioxygenases, structure-function analysis of the ethylene forming subclass of 2-oxoglutarate/Fe(II)-dependent dioxygenases, overview
evolution
the enzyme belongs to a subclass of 2-oxoglutarate/Fe(II) dependent dioxygenases, structure-function analysis of the ethylene forming subclass of 2-oxoglutarate/Fe(II)-dependent dioxygenases,overview
evolution
-
ethylene-forming enzyme (EFE) is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily
-
evolution
-
enzyme EFE is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. It contains a double-stranded beta-helix (DSBH, also known as the jellyroll or cupin fold) core typically found in members of the Fe(II)/2OG-dependent oxygenases
-
metabolism
-
analysis enzyme EFE reaction and cellular carbon flux, overview
metabolism
analysis enzyme EFE reaction and cellular carbon flux, overview
metabolism
analysis enzyme EFE reaction and cellular carbon flux, overview
metabolism
analysis enzyme EFE reaction and cellular carbon flux, overview
metabolism
-
analysis enzyme EFE reaction and cellular carbon flux, overview
-
physiological function
a non-heme Fe(II)- and 2-oxoglutarate-dependent ethylene-forming enzyme, EFE converts 2-oxoglutarate into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of L-arginine driven by the oxidative decarboxylation of 2-oxoglutarate to form succinate and CO2
physiological function
-
in the presence of O2, the enzyme catalyzes ethylene formation from the substrates 2-oxoglutarate and L-arginine
physiological function
the enzyme is reported to simultaneously catalyze the conversion of 2OG into ethylene plus three CO2 and the Cdelta hydroxylation of L-arginine (L-Arg) while oxidatively decarboxylating 2OG to form succinate and carbon dioxide. The enzyme produces ethylene, a gas that is widely used as a building block in the production of various plastics, detergents, surfactants, antifreeze, solvents, and other important industrial materials. And ethylene is a plant hormone that plays an important role in growth and development. The ethylene-forming reaction is not intrinsically linked to L-Arg hydroxylation
physiological function
the ethylene-forming enzyme (Efe) from Pseudomonas syringae pv. phaseolicola PK2 (the Kudzu strain) catalyzes the conversion of the ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene
physiological function
-
the enzyme is reported to simultaneously catalyze the conversion of 2OG into ethylene plus three CO2 and the Cdelta hydroxylation of L-arginine (L-Arg) while oxidatively decarboxylating 2OG to form succinate and carbon dioxide. The enzyme produces ethylene, a gas that is widely used as a building block in the production of various plastics, detergents, surfactants, antifreeze, solvents, and other important industrial materials. And ethylene is a plant hormone that plays an important role in growth and development. The ethylene-forming reaction is not intrinsically linked to L-Arg hydroxylation
-
physiological function
-
a non-heme Fe(II)- and 2-oxoglutarate-dependent ethylene-forming enzyme, EFE converts 2-oxoglutarate into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of L-arginine driven by the oxidative decarboxylation of 2-oxoglutarate to form succinate and CO2
-
physiological function
-
the ethylene-forming enzyme (Efe) from Pseudomonas syringae pv. phaseolicola PK2 (the Kudzu strain) catalyzes the conversion of the ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene
-
additional information
three of the amino acids correlating with ethylene production are located in the predicted 2-oxoglutarate binding domain, a protein domain specific for the EFE-class that is essential for activity. Residues H189, D191 and H268 are responsible for binding the Fe(II) ligand
additional information
three of the amino acids correlating with ethylene production are located in the predicted 2-oxoglutarate binding domain, a protein domain specific for the EFE-class that is essential for activity. Residues H189, D191 and H268 are responsible for binding the Fe(II) ligand
Show AA Sequence and Transmembrane Helices (2077 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
36000
39370
recombinant detagged enzyme, gel filtration
42000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
the overall PsEFE fold comprises 10 alpha-helices and 14 beta-strands, of which eight beta-strands (I-VIII) form the major and minor beta-sheets of the conserved distorted double-stranded beta helix (DSBH): the 2-oxoglutarate oxygenase characteristic fold. beta-Strands beta1 and beta2 at the N-terminus extend the major beta-sheet at the end of the DSBH away from the active site, beta-strands beta3 and beta6 extend the other end of the major beta-sheet close to the active site. alpha-Helices alpha2 and alpha5 bind across the surface of the major beta-sheet and likely stabilize it. A loop region (residues 80-93), located between beta3 and beta6, which harbors beta4 and beta5, acts as a lid partially covering the active site and provides residues that bind the L-Arg cofactor/substrate. Three alpha-helices (alpha8, alpha9, alpha10) at the C-terminus also contribute to the active site
monomer
1 * 40000, recombinant detagged enzyme, SDS-PAGE, 1 * 39670, recombinant detagged enzyme, mass spectrometry
monomer
-
1 * 40000, recombinant detagged enzyme, SDS-PAGE, 1 * 39670, recombinant detagged enzyme, mass spectrometry
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
analysis of crystal structure of the enzyme in complex with several ligands, detailed overview
purified recombinant enzyme in three structures: of enzyme in complex with manganese and 2-oxoglutarate, of enzyme in complex with with manganese and bis-Tris-propane buffer, and enzyme in complex with iron, L-Arg, and N-oxalylglycine, hanging drop vapour diffusion method, mixing of 0.003 ml of 12-20 mg/ml protein solution with 0.003 ml of reservoir solution containing 17.5-25% w/v PEG 3350 and PEG 6000, 0.1 M bis-Tris-propane, pH 7.0, 0.04 M sodium/potassium phosphate, 3-5 mM MnCl2, and with or without 10 mM 2-oxoglutarate, and equilibration against 0.5 ml reservoir solution, at 20°, microseeding, method optimization, X-ray diffraction structure determination and analysis at 1.08-1.55 A resolution, single-wavelength anomalous diffraction data obtained from selenomethionine-derivatized PsEFE:Mn:bis-Tris-propane crystals, structure modeling
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A198V
site-directed mutagenesis, the mutant produces large amounts of L-DELTA1-pyrroline-5-carboxylate but very little ethylene
A199G
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
A281V
site-directed mutagenesis, the mutant produces low levels of products in comparison to the wild-type enzyme
C280F
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
D191A
site-directed mutagenesis, inactive mutant
D191E
the D191E variant degrades L-Arg and 2-oxoglutarate to pyrroline-5-carboxylate (again detected after reduction to proline and Fmoc derivatization) and succinate nearly stoichiometrically, with only about 5% of the cosubstrate being fragmented to ethylene
E235D
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
E84D
site-directed mutagenesis, the mutant does not produce ethylene
E84Q
site-directed mutagenesis, the mutant does not produce ethylene
F278Y
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
F283A
site-directed mutagenesis, replacing F283 by tryptophan, tyrosine, arginine, alanine, and valine leads to the near elimination of ethylene production
F283R
site-directed mutagenesis, replacing F283 by tryptophan, tyrosine, arginine, alanine, and valine leads to the near elimination of ethylene production
F283V
site-directed mutagenesis, replacing F283 by tryptophan, tyrosine, arginine, alanine, and valine leads to the near elimination of ethylene production
F283Y
site-directed mutagenesis, replacing F283 by tryptophan, tyrosine, arginine, alanine, and valine leads to the near elimination of ethylene production
H116Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
H169Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
H189A
site-directed mutagenesis, inactive mutant
H233A
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
H233Q
site-directed mutagenesis, inactive mutant
H268A
site-directed mutagenesis, inactive mutant
H284Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
H309Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
I254M
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
I304N
site-directed mutagenesis, inactive mutant
I322V
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
L22M
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
R171A
R171K
site-directed mutagenesis, the mutant does not produce ethylene
R236S
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
R277A
site-directed mutagenesis, the mutant is expressed in inclusion bodies
R316A
site-directed mutagenesis, the mutant shows reduced ethylene production compared to the wild-type enzyme
R316K
site-directed mutagenesis, the mutant shows reduced ethylene production compared to the wild-type enzyme
V172T
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
V196F
site-directed mutagenesis, the mutant is expressed in inclusion bodies
V212Y/E213S
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Y172F
site-directed mutagenesis, the mutant shows reduced ethylene production compared to the wild-type enzyme
A198V
-
site-directed mutagenesis, the mutant produces large amounts of L-DELTA1-pyrroline-5-carboxylate but very little ethylene
-
F283Y
-
site-directed mutagenesis, replacing F283 by tryptophan, tyrosine, arginine, alanine, and valine leads to the near elimination of ethylene production
-
H309Q
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
-
R171A
-
site-directed mutagenesis, the mutant is soluble, it produces no detectable ethylene
-
V196F
-
site-directed mutagenesis, the mutant is expressed in inclusion bodies
-
H116Q
kcat value decreases to 2.4% of wild-type. Mutant is more thermolabile than wild-type
H168Q
kcat value decreases to 3% of wild-type. Mutant is more thermolabile than wild-type
H169Q
kcat value decreases to 9.3% of wild-type. Mutant is more thermolabile than wild-type
H284Q
kcat value decreases to 2% of wild-type. Mutant is more thermolabile than wild-type
H309Q
kcat value decreases to 3.3% of wild-type. Mutant is more thermolabile than wild-type
A199G
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
C280F
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
E235D
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
F278Y
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
H233A
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
I254M
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
I322V
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
L22M
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
R236S
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
V172T
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
V212Y/E213S
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
additional information
R171A
site-directed mutagenesis, the mutant does not produce ethylene
R171A
site-directed mutagenesis, the mutant is soluble, it produces no detectable ethylene
additional information
a loop deletion mutant is inactive
additional information
construction of a glycogen-synthesis knockout mutant (DELTAglgC) to raise the intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene is formed. Introduction of the ethylene biosynthetic pathway in mutant DELTAglgC. Under nitrogen limiting conditions, the glycogen knockout strain has increased intracellular 2-oxoglutarate levels, but the ethylene production is lower in the mutant strain than in the wild-type strain
additional information
-
construction of a glycogen-synthesis knockout mutant (DELTAglgC) to raise the intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene is formed. Introduction of the ethylene biosynthetic pathway in mutant DELTAglgC. Under nitrogen limiting conditions, the glycogen knockout strain has increased intracellular 2-oxoglutarate levels, but the ethylene production is lower in the mutant strain than in the wild-type strain
-
additional information
introduction of a gene encoding a chimeric protein consisting of EFE and beta-glucuronidase GUS into the tobacco genome using a binary vector which directs expression of the EFE-GUS fusion protein under the control of constitutive promoter of cauliflower mosaic virus 35S RNA
additional information
-
improvement of ethylene forming enzyme expression in Escherichia coli, method optimization, overview. Because L-arginine is a co-substrate of 2-oxoglutarate for the production of ethylene, L-arginine availability is improved via deregulation of L-arginine biosynthesis. In Escherichia coli, arginine biosynthesis is controlled by a regulatory protein encoded by argR. Knockout of gene argR alleviates regulation of arginine biosynthesis resulting in increased arginine availability. The removal of arginine biosynthesis regulation in the DELTAargR Escherichia coli mutant strain improves production of ethylene by 36% compared to the wild-type strain. Knockout of both small and large subunits of the native glutamate synthase (gltBD) might increase 2-oxoglutarate accumulation and production of ethylene. The removal of a third 2-oxoglutarate-consuming pathway, 2-oxoglutarate dehydrogenase (sucA), is also explored. This enzyme catalyzes the formation of succinyl-CoA and CO2 from AKG, and deletion of sucA results in increased 2-oxoglutarate levels in batch culture
additional information
a loop deletion mutant is inactive
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli strain BL21(DE3) to near homogeneity by affinityy chromatography, desalting gel filtration, tag cleavage by human SenP2 protease, followed by another step of affinityy chromatography, and gel filtration
recombinant His-tagged enzyme from Escherichia coli strain BL21 Gold (DE3) by nickel affinity chromatography, tag cleavage by a TEV protease mutant, and another step of nickel affinity chromatography, and dialysis of the flow through
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, sequence comparisons with Pseudomonas digitatum and Pseudomonas chrysogenum, recombinant expression in Saccharomyces cerevisiae
expressed in Saccharomyces cerevisae. Different cultivation factors on ethylene formation in Saccharomyces cerevisiae expressing the EFE in continuous cultures are investigated. Main finding is that oxygen availability is crucial for ethylene production. By employing three different nitrogen sources it is shown that the nitrogen source available can both improve and impair the ethylene productivity. N-Source/yield ethylene (microgram/g glucose): (NH4)2SO4/164, glutamate/233, glutamate+arginine/96.8
-
gene efe, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis and tree
gene efe, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis and tree, heterologous expression of the single efe gene from Pseudomonas syringae results in ethylene production in a number of hosts including Escherichia coli, Saccharomyces cerevisiae, Pseudomonas putida, Trichoderma viride, Trichoderma reesei, tobacco, and cyanobacteria. Methods overview
gene efe, large scale expression of His6-tagged enzyme in Escherichia coli strain BL21 Gold (DE3), method optimization and evaluation
gene efe, recombinant enzyme expression in Synechocystis sp. strain PCC 6803, stable ethylene production through the integration of a codon-optimized version of the efe gene under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5'-AGGAGG-3) as the ribosome-binding site, at the slr0168 neutral site. Increase in ethylene production is achieved twofold by RBS screening, improvement of ethylene production from a single gene copy of efe, using multiple tandem promoters and by putting our best construct on an RSF1010-based broad-hostself-replicating plasmid, which has a higher copy number than the genome
gene efe, recombinant expression in Escherichia coli strain MG1655, importance of promoter strength on the expression of enzyme EFE in Escherichia coli with stronger promoters producing elevated levels of ethylene, e.g. the Amaranthus hybridus chloroplast psbA promoter (PpsbA), expression method optimization, overview
-
gene efe, recombinant expression of N-terminally His-tagged or N-terminally His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)
His-tagged form of enzyme is generated in Escherichia coli BL21 Gold (DE3) cells
-
recombinant expression of wild-type and mutant enzymes
DNA and amino acid sequence determination and analysis, sequence comparisons with Pseudomonas digitatum and Pseudomonas chrysogenum, recombinant expression in Saccharomyces cerevisiae
DNA and amino acid sequence determination and analysis, sequence comparisons with Pseudomonas digitatum and Pseudomonas chrysogenum, recombinant expression in Saccharomyces cerevisiae
gene efe, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis and tree
-
gene efe, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis and tree
gene efe, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis and tree
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
agriculture
introduction of a gene encoding a chimeric protein consisting of EFE and beta-glucuronidase GUS into the tobacco genome using a binary vector which directs expression of the EFE-beta-glucuronidase fusion protein under the control of constitutive promoter of cauliflower mosaic virus 35S RNA. Transgenic plants produce ethylene at consistently higher rates than the untransformed plant, and their beta-glucuronidase activities are expressed in different tissues. A significant dwarf morphology observed in the transgenic tobacco displaying the highest ethylene production resembles the phenotype of a wild-type plant exposed to excess ethylene
biotechnology
synthesis
-
biological ethylene production can be achieved via expression of the ethylene-forming enzyme (EFE), found in some bacteria and fungi. It has the potential to provide a sustainable alternative to steam cracking. Ethylene is an important industrial compound for the production of a wide variety of plastics and chemicals
biotechnology
-
different cultivation factors on ethylene formation in Saccharomyces cerevisiae expressing the EFE in continuous cultures is investigated. Main finding is that oxygen availability is crucial for ethylene production. By employing three different nitrogen sources it is shown that the nitrogen source available can both improve and impair the ethylene productivity
biotechnology
EFE is a promising biotechnology target because the expression of a single gene is sufficient for ethylene production in the absence of toxic intermediates
biotechnology
EFE is a promising biotechnology target because the expression of a single gene is sufficient for ethylene production in the absence of toxic intermediates
biotechnology
-
EFE is a promising biotechnology target because the expression of a single gene is sufficient for ethylene production in the absence of toxic intermediates
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Fukuda, H.; Ogawa, T.; Tazaki, M.; Nagahama, K.; Fujii, T.; Tanase, S.; Morino, Y.
Two reactions are simultaneously catalyzed by a single enzyme: The arginine-dependent simultaneous formation of two products, ethylene and succinate, from 2-oxoglutarate by an enzyme from Pseudomonas syringae
Biochem. Biophys. Res. Commun.
188
483-489
1992
Pseudomonas syringae (P32021)
brenda
Fukuda, H.; Ogawa, T.; Ishihara, K.; Fujii, T.; Nagahama, K.; Omata, T.; Inoue, Y.; Tanase, S.; Morino, Y.
Molecular cloning in Escherichia coli, expression, and nucleotide sequence of the gene for the ethylene-forming enzyme of Pseudomonas syringae pv. phaseolicola PK2
Biochem. Biophys. Res. Commun.
188
826-832
1992
Pseudomonas syringae (P32021)
brenda
Nagahama, K.; Yoshino, K.; Matsuoka, M.; Tanase, S.; Ogawa, T.; Fukuda, H.
Site-directed mutagenesis of histidine residues in the ethylene-forming enzyme from Pseudomonas syringae
J. Ferment. Bioeng.
85
255-258
1998
Pseudomonas syringae (P32021)
-
brenda
Nagahama, K.; Ogawa, T.; Fujii, T.; Tazaki, M.; Tanase, S.; Morino, Y.; Fukuda, H.
Purification and properties of an ethylene-forming enzyme from Pseudomonas syringae pv. Phaseolicola PK2
J. Gen. Microbiol.
137
2281-2286
1991
Pseudomonas syringae (P32021)
brenda
Araki, S.; Matsuoka, M.; Tanaka, M.; Ogawa, T.
Ethylene formation and phenotypic analysis of transgenic tobacco plants expressing a bacterial ethylene-forming enzyme
Plant Cell Physiol.
41
327-334
2000
Pseudomonas syringae (P32021)
brenda
Johansson, N.; Quehl, P.; Norbeck, J.; Larsson, C.
Identification of factors for improved ethylene production via the ethylene forming enzyme in chemostat cultures of Saccharomyces cerevisiae
Microb. Cell Fact.
12
89
2013
Pseudomonas syringae
brenda
Martinez, S.; Hausinger, R.P.
Biochemical and spectroscopic characterization of the non-heme Fe(II)- and 2-oxoglutarate-dependent ethylene-forming enzyme from Pseudomonas syringae pv. phaseolicola PK2
Biochemistry
55
5989-5999
2016
Pseudomonas savastanoi pv. phaseolicola (P32021), Pseudomonas savastanoi pv. phaseolicola PK2 (P32021)
brenda
Eckert, C.; Xu, W.; Xiong, W.; Lynch, S.; Ungerer, J.; Tao, L.; Gill, R.; Maness, P.; Yu, J.
Ethylene-forming enzyme and bioethylene production
Biotechnol. Biofuels
7
33
2014
Penicillium digitatum, Pseudomonas savastanoi pv. phaseolicola (P32021), Pseudomonas savastanoi pv. glycinea (Q7BS32), Ralstonia solanacearum (Q8XPV7), Pseudomonas savastanoi pv. phaseolicola PK2 (P32021)
brenda
Martinez, S.; Fellner, M.; Herr, C.Q.; Ritchie, A.; Hu, J.; Hausinger, R.P.
Structures and mechanisms of the non-heme Fe(II)- and 2-oxoglutarate-dependent ethylene-forming enzyme Substrate binding creates a twist
J. Am. Chem. Soc.
139
11980-11988
2017
Pseudomonas savastanoi pv. phaseolicola (P32021), Pseudomonas savastanoi pv. phaseolicola PK2 (P32021)
brenda
Veetil, V.P.; Angermayr, S.A.; Hellingwerf, K.J.
Ethylene production with engineered Synechocystis sp PCC 6803 strains
Microb. Cell Fact.
16
34
2017
Pseudomonas savastanoi pv. phaseolicola (Q549K5), Pseudomonas savastanoi pv. phaseolicola PK2 (Q549K5)
brenda
Zhang, Z.; Smart, T.J.; Choi, H.; Hardy, F.; Lohans, C.T.; Abboud, M.I.; Richardson, M.S.W.; Paton, R.S.; McDonough, M.A.; Schofield, C.J.
Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate
Proc. Natl. Acad. Sci. USA
114
4667-4672
2017
Pseudomonas savastanoi pv. phaseolicola (P32021)
brenda
Lynch, S.; Eckert, C.; Yu, J.; Gill, R.; Maness, P.C.
Overcoming substrate limitations for improved production of ethylene in E. coli
Biotechnol. Biofuels
9
3-13
2016
Pseudomonas syringae
brenda
Johansson, N.; Persson, K.; Norbeck, J.; Larsson, C.
Expression of NADH-oxidases enhances ethylene productivity in Saccharomyces cerevisiae expressing the bacterial EFE
Biotechnol. Bioprocess Eng.
22
195-199
2017
Pseudomonas savastanoi pv. phaseolicola (P32021), Pseudomonas syringae pv. pisi (Q9Z3T0)
-
brenda
Li, M.; Martinez, S.; Hausinger, R.P.; Emerson, J.P.
Thermodynamics of iron(II) and substrate binding to the ethylene-forming enzyme
Biochemistry
57
5696-5705
2018
Pseudomonas syringae
brenda
Copeland, R.A.; Davis, K.M.; Shoda, T.K.C.; Blaesi, E.J.; Boal, A.K.; Krebs, C.; Bollinger, J.M.
An iron(IV)-oxo intermediate initiating L-arginine oxidation but not ethylene production by the 2-oxoglutarate-dependent oxygenase, ethylene-forming enzyme
J. Am. Chem. Soc.
143
2293-2303
2021
Pseudomonas savastanoi pv. phaseolicola (P32021)
brenda
Xue, J.; Lu, J.; Lai, W.
Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme selectivity of ethylene-formation versusl-Arg hydroxylation
Phys. Chem. Chem. Phys.
21
9957-9968
2019
Pseudomonas savastanoi pv. phaseolicola (P32021)
brenda
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