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Enzyme Nomenclature
Information on EC 1.13.11.72 - 2-hydroxyethylphosphonate dioxygenase
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The expected taxonomic range for this enzyme is: Streptomyces viridochromogenes
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EC NUMBER 
COMMENTARY 
1.13.11.72
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RECOMMENDED NAME
GeneOntology No.
2-hydroxyethylphosphonate dioxygenase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
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2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
catalytic mechanism
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2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
the reaction proceeds via a transient iron(IV)-oxo (ferryl) complex, a mechanism that involves activation of an O-H bond by the ferryl complex is proposed. The isotope-sensitive C-H-cleavage step is not primarily rate-limiting for the overall catalytic cycle. The reaction does exhibit a significant 2H-kinetic isotope effect on kcat/Km for O2, which implies reversible formation of the C-H-cleaving intermediate
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2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species, catalytic mechanism, detailed overview
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2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
catalytic mechanism; initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species, catalytic mechanism, detailed overview; the reaction proceeds via a transient iron(IV)-oxo (ferryl) complex, a mechanism that involves activation of an O-H bond by the ferryl complex is proposed. The isotope-sensitive C-H-cleavage step is not primarily rate-limiting for the overall catalytic cycle. The reaction does exhibit a significant 2H-kinetic isotope effect on kcat/Km for O2, which implies reversible formation of the C-H-cleaving intermediate
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
2-hydroxyethylphosphonate:O2 1,2-oxidoreductase (hydroxymethylphosphonate forming)
Requires non-heme-Fe(II). Isolated from some bacteria including Streptomyces hygroscopicus and Streptomyces viridochromogenes. The pro-R hydrogen at C-2 of the ethyl group is retained by the formate ion. Any stereochemistry at C-1 of the ethyl group is lost. One atom from dioxygen is present in each product. Involved in phosphinothricin biosynthesis.
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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UniProt
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
additional information
evolution
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2-hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are non-heme iron oxygenases that both catalyze the carbon-carbon bond cleavage of 2-hydroxyethylphosphonate but generate different products. Both HEPD and MPnS generate a methylphosphonate radical. Substrate labeling experiments lead to a mechanistic hypothesis in which the fate of a common intermediate determines product identity, overview. Primary sequences and homology modeling suggest that the architectures of the active sites of HEPD and MPnS are similar
evolution
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one group of mononuclear non-heme iron-dependent enzymes includes 2-hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS, EC 1.13.11.73) that both carry out the oxidative cleavage of the carbon-carbon bond of 2-hydroxyethylphosphonate but generate different products. Common properties include the initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species. Sequence homology between HEPD and MPnS combined with identical requirements for catalysis suggests a consensus mechanism in which product identity is determined by branching at an intermediate in the catalytic cycle
evolution
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2-hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are non-heme iron oxygenases that both catalyze the carbon-carbon bond cleavage of 2-hydroxyethylphosphonate but generate different products. Both HEPD and MPnS generate a methylphosphonate radical. Substrate labeling experiments lead to a mechanistic hypothesis in which the fate of a common intermediate determines product identity, overview. Primary sequences and homology modeling suggest that the architectures of the active sites of HEPD and MPnS are similar; one group of mononuclear non-heme iron-dependent enzymes includes 2-hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS, EC 1.13.11.73) that both carry out the oxidative cleavage of the carbon-carbon bond of 2-hydroxyethylphosphonate but generate different products. Common properties include the initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species. Sequence homology between HEPD and MPnS combined with identical requirements for catalysis suggests a consensus mechanism in which product identity is determined by branching at an intermediate in the catalytic cycle
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physiological function
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2-hydroxyethylphosphonate dioxygenase (HEPD) cleaves the C1-C2 bond of its substrate to afford hydroxymethylphosphonate on the biosynthetic pathway to the commercial herbicide phosphinothricin
physiological function
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2-hydroxyethylphosphonate dioxygenase (HEPD) cleaves the C1-C2 bond of its substrate to afford hydroxymethylphosphonate on the biosynthetic pathway to the commercial herbicide phosphinothricin
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additional information
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the active site metal is coordinated by 2-His-1-Glu on one face of a pseudooctrahedron
additional information
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the active site metal is coordinated by 2-His-1-Glu on one face of a pseudooctrahedron
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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
(2R)-hydroxypropylphosphonate + O2
2-oxopropylphosphonate + hydroxymethylphosphonate + acetate
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substrate partitions between conversion to 2-oxopropylphosphonate and hydroxymethylphosphonate
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?
(R)-2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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product is almost racemic
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?
(S)-2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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product is almost racemic
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?
1-hydroxy-2,2,2-trifluoroethylphosphonate + O2
trifluoroacetylphosphonate
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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all four electrons required for reduction of O2 are provided by the substrate. Occurence of an intermediate species in which oxygen derived from O2 exchanges with water
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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catalytic cycle is based on concatenated bifurcations. The first bifurcation is based on the abstraction of hydrogen atoms from the substrate, which leads to a distal or proximal hydroperoxo species Fe-OOH or Fe-(OH)O. The second and the third bifurcations refer to the carbon-carbon bond cleavage reaction achieved through a tridentate intermediate, or employing a proton-shuttle assisted mechanism, in which the residue Glu176 or the FeIV O group serves as a general base. The reaction directions seem to be tunable and show significant environment dependence
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2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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in the reaction mechanism water molecules serve as an oxygen source in the generation of mononuclear nonheme iron oxo complexes, taking part in the catalytic cycle before the carbon-carbon bond cleavage process. After the dioxygen is bound to the iron center, the dioxygen-bound species Fe-O2 is generated. The abstraction of hydrogen atom from the substrate leads to a distal or proximal hydroperoxo species Fe(III)-OOH. This is the rate-limiting step, which has an energy barrier of 21 and 18 kcal/mol for distal and proximal H-abstraction processes, respectively. The second step is the cleavage of the O-O bond, and the carbon-carbon bond is broken subsequently. In this step, a tridentate binding species and a Fe(IV) sigmaO species are important intermediates to break the carbon-carbon bond. In the third step, the formic acid and the intermediate CH2PO2(OH)- radical are generated. Finally, 2-hydroxyethylphosphonate is converted to hydroxymethylphosphonate, and the formate or formic acid is formed
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2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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mechanism involves removal of the pro-S hydrogen at C2 and the loss of stereochemical information at C1. Thus, the hydroperoxylation mechanism, previously proposed as the product of a Criegee rearrangement, cannot be operational for conversion of 2-hydroxyethylphosphonate
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2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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an irreversible step involving O2
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ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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the reaction proceeds via a transient iron(IV)-oxo (ferryl) complex, the mechanism involves activation of an O-H bond by the ferryl complex. Maximal accumulation of the intermediate requires both the presence of deuterium in the substrate and, importantly, the use of 2H2O as solvent
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2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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the reaction proceeds via a transient iron(IV)-oxo (ferryl) complex, the mechanism involves activation of an O-H bond by the ferryl complex. Maximal accumulation of the intermediate requires both the presence of deuterium in the substrate and, importantly, the use of 2H2O as solvent
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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an irreversible step involving O2
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ir
additional information
?
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proper binding of 2-hydroxyethylphosphonate is important for O2 activation and the enzyme uses a compulsory binding order with 2-hydroxyethylphosphonate binding before O2. In the mechanism, a hydroperoxylation process is followed by a Criegee rearrangement and hydrolysis to form hydroxymethylphosphonate. Thereafter, the P-C bond in the product can be transiently broken, generating phosphite and formaldehyde in the active site of the enzyme. If the formaldehyde is able to rotate along the C=O bond, then phosphite can attack either face of the carbonyl group resulting in a loss of stereochemistry
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additional information
?
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reaction starts with H-abstraction from the C2 position of 2-hydroxyethylphosphonate by a ferric superoxide-type intermediate. The resultant Fe(II)-OOH intermediate may follow either a hydroperoxylation or hydroxylation pathway, the former process being energetically more favorable. In the hydroperoxylation pathway, a ferrous-alkylhydroperoxo intermediate is formed, and then its O-O bond is homolytically cleaved to yield a complex of ferric hydroxide with a gem-diol radical. Subsequent C-C bond cleavage within the gem-diol leads to formation of an R-CH2 radical species and one of the two products, i.e., formic acid. The R-CH2 radical then intramolecularly forms a C-O bond with the ferric hydroxide to provide the other product, hydroxymethylphosphonate. The overall reaction pathway requires ferric superoxide and ferric hydroxide intermediates
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additional information
?
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results provide strong support for a mechanism that proceeds by hydroperoxylation followed by a Criegee rearrangement with a phosphorus-based migrating group and requires that the O-O bond of molecular oxygen is not cleaved prior to substrate activation. No substrate: O-formyl-hydroxymethylphosphonate, (2S)-hydroxypropylphosphonate
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additional information
?
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HEPD oxidizes a relatively unactivated substrate that cannot easily facilitate O2 activation. 2-Hydroxyethylphosphonate does not contain a thiol group that upon binding to the iron can activate it for catalysis, nor does it contain an 2-oxo acid functionality
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additional information
?
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HEPD oxidizes a relatively unactivated substrate that cannot easily facilitate O2 activation. 2-Hydroxyethylphosphonate does not contain a thiol group that upon binding to the iron can activate it for catalysis, nor does it contain an 2-oxo acid functionality
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
Q5IW40
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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ir
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Iron
Fe2+
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a non-heme iron oxygenase, Fe2+ is required for catalysis
Fe2+
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required for catalysis, the mechanism involves activation of an O-H bond by the ferryl complex
Iron
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the overall reaction pathway requires ferric superoxide and ferric hydroxide intermediates
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
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steady-state Michaelis-Menten kinetics of wild-type enzyme and mutant E176H
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additional information
additional information
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stopped-flow and multi-turnover steady-state kinetics
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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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PDB
SCOP
CATH
UNIPROT
ORGANISM
Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494);
Q5IW40
Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494);
Q5IW40
Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494);
Q5IW40
Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494);
Q5IW40
Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494);
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in vitro reconstitution of activity and determination of the crystal structure of Cd2+-substituted PhpD in complex with the 2-hydroxyethylphosphonate substrate
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purified recombinant enzyme mutant E176H, X-ray diffraction structure determination and analysis at 1.75 A resolution
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to 1.8 A resolution. The overall structure consists of imperfect tandem repeats of a bi-domain architecture. Each of the repeats is composed of an all-alpha-helical domain linked to a beta-barrel fold characteristic of the cupin superfamily. A Cd(II) ion is situated at the base of the active site and is coordinated by residues His 129, Glu 176 and His 182
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes from Escherichia coli
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant expression of wild-type and mutant enzymes in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E176A
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site-directed mutagenesis, the mutant enzyme shows similar activity as the wild-type enzyme. Like the wild-type enzyme, the mutant HEPD-E176A produces hydroxymethylphosphonate and formate as its only detectable products upon incubation with Fe(II), hydroxyethylphosphonate, and O2
E176H
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site-directed mutagenesis, the mutant is bifunctional exhibiting the activity of both 2-hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS, EC 1.13.11.73). The product distribution of the mutant is sensitive to a substrate isotope effect, consistent with an isotope-sensitive branching mechanism involving a common intermediate. The introduced histidine does not coordinate the active site metal, unlike the iron-binding glutamate it replaces. More HEPD activity is observed when the reaction is carried out with (R)-2-[2-2H1]-hydroxyethylphosphonate
R90A
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large decrease in ratio kcat/Km, mutant cannot be saturated in O2
Y98F
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large decrease in ratio kcat/Km, mutant cannot be saturated in O2. Mutant produces methylphosphonate as a minor side product
E176A
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site-directed mutagenesis, the mutant enzyme shows similar activity as the wild-type enzyme. Like the wild-type enzyme, the mutant HEPD-E176A produces hydroxymethylphosphonate and formate as its only detectable products upon incubation with Fe(II), hydroxyethylphosphonate, and O2
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E176H
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site-directed mutagenesis, the mutant is bifunctional exhibiting the activity of both 2-hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS, EC 1.13.11.73). The product distribution of the mutant is sensitive to a substrate isotope effect, consistent with an isotope-sensitive branching mechanism involving a common intermediate. The introduced histidine does not coordinate the active site metal, unlike the iron-binding glutamate it replaces. More HEPD activity is observed when the reaction is carried out with (R)-2-[2-2H1]-hydroxyethylphosphonate
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LINKS TO OTHER DATABASES (specific for EC-Number 1.13.11.72)
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