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Enzyme Nomenclature
Information on EC 1.13.11.72 - 2-hydroxyethylphosphonate dioxygenase
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1.13.11.72 2-hydroxyethylphosphonate dioxygenaseIUBMB Comments
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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The enzyme appears in viruses and cellular organisms
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
HEPD
phpD
HEPD
-
-
-
-
phpD
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
-
-
-
-
2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
catalytic mechanism
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
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
2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
catalytic mechanism
-
-
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
-
-
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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PATHWAY SOURCE
PATHWAYS
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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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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
-
substrate partitions between conversion to 2-oxopropylphosphonate and hydroxymethylphosphonate
-
?
(R)-2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
product is almost racemic
-
?
(S)-2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
product is almost racemic
-
?
1-hydroxy-2,2,2-trifluoroethylphosphonate + O2
trifluoroacetylphosphonate
-
-
-
?
hydroxymethylphosphonate + O2
phosphate + formate
-
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
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
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
an irreversible step involving O2
-
-
ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
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
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
an irreversible step involving O2
-
-
ir
additional information
?
-
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
-
-
?
additional information
?
-
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
-
-
?
additional information
?
-
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
-
-
?
additional information
?
-
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
-
-
?
additional information
?
-
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 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
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
ir
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
?
2-hydroxyethylphosphonate + O2
hydroxymethylphosphonate + formate
-
-
-
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+
a non-heme iron oxygenase, Fe2+ is required for catalysis
Fe2+
required for catalysis, the mechanism involves activation of an O-H bond by the ferryl complex
Iron
the overall reaction pathway requires ferric superoxide and ferric hydroxide intermediates
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0098
2-hydroxyethylphosphonate
wild-type, pH 7.5, 20°C
0.06
2-hydroxyethylphosphonate
mutant R90K, pH 7.5, 20°C
0.69
2-hydroxyethylphosphonate
mutant R90A, pH 7.5, 20°C
0.8
2-hydroxyethylphosphonate
mutant Y98F, pH 7.5, 20°C
additional information
additional information
steady-state Michaelis-Menten kinetics of wild-type enzyme and mutant E176H
-
additional information
additional information
stopped-flow and multi-turnover steady-state kinetics
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.35
2-hydroxyethylphosphonate
wild-type, pH 7.5, 20°C
0.81
2-hydroxyethylphosphonate
mutant R90K, pH 7.5, 20°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
13
2-hydroxyethylphosphonate
mutant R90K, pH 7.5, 20°C
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
physiological function
additional information
evolution
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
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
-
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
-
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
-
physiological function
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
-
2-hydroxyethylphosphonate dioxygenase (HEPD) cleaves the C1-C2 bond of its substrate to afford hydroxymethylphosphonate on the biosynthetic pathway to the commercial herbicide phosphinothricin
-
additional information
the active site metal is coordinated by 2-His-1-Glu on one face of a pseudooctrahedron
additional information
-
the active site metal is coordinated by 2-His-1-Glu on one face of a pseudooctrahedron
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). HEPD_STRVT
Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494)
443
0
48091
Swiss-Prot
-
A0A2S6QAZ1_9PROT
453
0
50666
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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SUBUNIT
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
purified recombinant enzyme mutant E176H, X-ray diffraction structure determination and analysis at 1.75 A resolution
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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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E176A
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
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
large decrease in ratio kcat/Km, mutant cannot be saturated in O2
Y98F
large decrease in ratio kcat/Km, mutant cannot be saturated in O2. Mutant produces methylphosphonate as a minor side product
E176A
-
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
-
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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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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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Peck, S.C.; Cooke, H.A.; Cicchillo, R.M.; Malova, P.; Hammerschmidt, F.; Nair, S.K.; van der Donk, W.A.
Mechanism and substrate recognition of 2-hydroxyethylphosphonate dioxygenase
Biochemistry
50
6598-6605
2011
Streptomyces viridochromogenes (Q5IW40)
brenda
Whitteck, J.T.; Cicchillo, R.M.; van der Donk, W.A.
Hydroperoxylation by hydroxyethylphosphonate dioxygenase
J. Am. Chem. Soc.
131
16225-16232
2009
Streptomyces viridochromogenes (Q5IW40)
brenda
Hirao, H.; Morokuma, K.
Ferric superoxide and ferric hydroxide are used in the catalytic mechanism of hydroxyethylphosphonate dioxygenase: a density functional theory investigation
J. Am. Chem. Soc.
132
17901-17909
2010
Streptomyces viridochromogenes (Q5IW40)
brenda
Whitteck, J.T.; Malova, P.; Peck, S.C.; Cicchillo, R.M.; Hammerschmidt, F.; van der Donk, W.A.
On the stereochemistry of 2-hydroxyethylphosphonate dioxygenase
J. Am. Chem. Soc.
133
4236-4239
2011
Streptomyces viridochromogenes (Q5IW40)
brenda
Du, L.; Gao, J.; Liu, Y.; Liu, C.
Water-dependent reaction pathways: an essential factor for the catalysis in HEPD enzyme
J. Phys. Chem. B
116
11837-11844
2012
Streptomyces viridochromogenes (Q5IW40)
brenda
Cicchillo, R.M.; Zhang, H.; Blodgett, J.A.; Whitteck, J.T.; Li, G.; Nair, S.K.; van der Donk, W.A.; Metcalf, W.W.
An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis
Nature
459
871-874
2009
Streptomyces viridochromogenes (Q5IW40)
brenda
Peck, S.C.; Chekan, J.R.; Ulrich, E.C.; Nair, S.K.; van der Donk, W.A.
A common late-stage intermediate in catalysis by 2-hydroxyethyl-phosphonate dioxygenase and methylphosphonate synthase
J. Am. Chem. Soc.
137
3217-3220
2015
Streptomyces viridochromogenes (Q5IW40), Streptomyces viridochromogenes DSM 40736 (Q5IW40)
brenda
Peck, S.C.; Wang, C.; Dassama, L.M.; Zhang, B.; Guo, Y.; Rajakovich, L.J.; Bollinger, J.M.; Krebs, C.; van der Donk, W.A.
O-H activation by an unexpected ferryl intermediate during catalysis by 2-hydroxyethylphosphonate dioxygenase
J. Am. Chem. Soc.
139
2045-2052
2017
Streptomyces viridochromogenes (Q5IW40), Streptomyces viridochromogenes DSM 40736 (Q5IW40)
brenda
Peck, S.C.; van der Donk, W.A.
Go it alone four-electron oxidations by mononuclear non-heme iron enzymes
J. Biol. Inorg. Chem.
22
381-394
2017
Streptomyces viridochromogenes (Q5IW40), Streptomyces viridochromogenes DSM 40736 (Q5IW40)
brenda
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