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Literature summary extracted from

  • Peck, S.C.; van der Donk, W.A.
    Go it alone four-electron oxidations by mononuclear non-heme iron enzymes (2017), J. Biol. Inorg. Chem., 22, 381-394 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.13.11.72 in vitro reconstitution of activity and determination of the crystal structure of Cd2+-substituted PhpD in complex with the 2-hydroxyethylphosphonate substrate Streptomyces viridochromogenes

Protein Variants

EC Number Protein Variants Comment Organism
1.14.99.50 Y377F site-directed mutagenesis, the single point mutation in EgtB completely uncouples substrate consumption from sulfoxide synthase activity with the native substrates hercynine and gamma-glutamyl cysteine, with EgtB exclusively oxidizing gamma-glutamyl cysteine to the sulfinic acid. Tyr377 is hydrogen bonded to a water molecule that coordinates to the iron Mycobacterium avium

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.13.11.72 Fe2+ a mononuclear non-heme iron-dependent enzyme Streptomyces viridochromogenes
1.13.11.73 Fe2+ a mononuclear non-heme iron-dependent enzyme. MPnS contains iron-binding residues at only the two histidines, raising the specter that either MPnS is a 2-His only enzyme or that the third ligand is not well conserved in the alignment Nitrosopumilus maritimus
1.14.99.50 Fe2+ non-heme iron, required for catalysis, the active site iron is coordinated by a 3-His facial triad rather than a 2-His-1-Glu ligand set Mycobacterium avium
1.14.99.52 Fe2+ non-heme iron, required for catalysis,residues in the HX3HXE motif might be involved in iron binding Erwinia tasmaniensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.13.11.72 2-hydroxyethylphosphonate + O2 Streptomyces viridochromogenes
-
hydroxymethylphosphonate + formate
-
ir
1.13.11.72 2-hydroxyethylphosphonate + O2 Streptomyces viridochromogenes DSM 40736
-
hydroxymethylphosphonate + formate
-
ir
1.13.11.73 2-hydroxyethylphosphonate + O2 Nitrosopumilus maritimus
-
methylphosphonate + HCO3-
-
ir
1.14.99.50 hercynine + gamma-L-glutamyl-L-cysteine + O2 Mycobacterium avium
-
gamma-L-glutamyl-S-(hercyn-2-yl)-L-cysteine S-oxide + H2O
-
?
1.14.99.52 L-histidine + L-cysteine + O2 Erwinia tasmaniensis
-
S-(L-histidin-5-yl)-L-cysteine S-oxide + H2O
-
?

Organism

EC Number Organism UniProt Comment Textmining
1.13.11.72 Streptomyces viridochromogenes Q5IW40
-
-
1.13.11.72 Streptomyces viridochromogenes DSM 40736 Q5IW40
-
-
1.13.11.73 Nitrosopumilus maritimus
-
-
-
1.14.99.50 Mycobacterium avium
-
-
-
1.14.99.52 Erwinia tasmaniensis
-
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
1.13.11.72 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 Streptomyces viridochromogenes
1.13.11.73 2-hydroxyethylphosphonate + O2 = methylphosphonate + HCO3- initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species, catalytic mechanism, detailed overview Nitrosopumilus maritimus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.13.11.72 2-hydroxyethylphosphonate + O2
-
Streptomyces viridochromogenes hydroxymethylphosphonate + formate
-
ir
1.13.11.72 2-hydroxyethylphosphonate + O2 an irreversible step involving O2 Streptomyces viridochromogenes hydroxymethylphosphonate + formate
-
ir
1.13.11.72 2-hydroxyethylphosphonate + O2
-
Streptomyces viridochromogenes DSM 40736 hydroxymethylphosphonate + formate
-
ir
1.13.11.72 2-hydroxyethylphosphonate + O2 an irreversible step involving O2 Streptomyces viridochromogenes DSM 40736 hydroxymethylphosphonate + formate
-
ir
1.13.11.72 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 Streptomyces viridochromogenes ?
-
?
1.13.11.72 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 Streptomyces viridochromogenes DSM 40736 ?
-
?
1.13.11.73 2-hydroxyethylphosphonate + O2
-
Nitrosopumilus maritimus methylphosphonate + HCO3-
-
ir
1.13.11.73 2-hydroxyethylphosphonate + O2 the pro-(R) hydrogen at C2 of 2-hydroxyethylphosphonate is quantitatively incorporated by enzyme MPnS into methylphosphonate. AN irreversible step involving O2 Nitrosopumilus maritimus methylphosphonate + HCO3-
-
ir
1.14.99.50 hercynine + gamma-L-glutamyl-L-cysteine + O2
-
Mycobacterium avium gamma-L-glutamyl-S-(hercyn-2-yl)-L-cysteine S-oxide + H2O
-
?
1.14.99.50 hercynine + gamma-L-glutamyl-L-cysteine + O2 sulfoxide incorporation at C2 by EgtB Mycobacterium avium gamma-L-glutamyl-S-(hercyn-2-yl)-L-cysteine S-oxide + H2O
-
?
1.14.99.50 additional information no activity with L-cysteine and L-histdine Mycobacterium avium ?
-
?
1.14.99.52 L-histidine + L-cysteine + O2
-
Erwinia tasmaniensis S-(L-histidin-5-yl)-L-cysteine S-oxide + H2O
-
?
1.14.99.52 L-histidine + L-cysteine + O2 OvoA modifies the C5 position of the imidazole ring of L-His, site selectivity of the transformation Erwinia tasmaniensis S-(L-histidin-5-yl)-L-cysteine S-oxide + H2O
-
?
1.14.99.52 additional information OvoA incubated with hercynine (the normal substrate for EgtB, EC 1.14.99.50) and cysteine produces primarily cysteine sulfinic acid, the product of cysteine dioxygenase-type chemistry, cf. EC 1.13.11.20 Erwinia tasmaniensis ?
-
?

Synonyms

EC Number Synonyms Comment Organism
1.13.11.72 HEPD
-
Streptomyces viridochromogenes
1.13.11.72 phpD
-
Streptomyces viridochromogenes
1.13.11.73 methylphosphonate synthase
-
Nitrosopumilus maritimus
1.13.11.73 mpnS
-
Nitrosopumilus maritimus
1.14.99.50 5-histidylcysteine sulfoxide synthase
-
Mycobacterium avium
1.14.99.50 EgtB
-
Mycobacterium avium
1.14.99.52 OvoA
-
Erwinia tasmaniensis
1.14.99.52 sulfoxide synthase
-
Erwinia tasmaniensis

General Information

EC Number General Information Comment Organism
1.13.11.72 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 Streptomyces viridochromogenes
1.13.11.72 additional information the active site metal is coordinated by 2-His-1-Glu on one face of a pseudooctrahedron Streptomyces viridochromogenes
1.13.11.73 evolution one group of mononuclear non-heme iron-dependent enzymes includes 2-hydroxyethylphosphonate dioxygenase (HEPD, EC 1.13.11.72) and methylphosphonate synthase (MPnS) 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 Nitrosopumilus maritimus
1.13.11.73 additional information apo MPnS homology modeling using the crystal structure of Cd2+-substituted HEPD, EC 1.13.11.72, in complex with substrate 2-hydroxyethylphosphonate, PDB ID 3GBF Nitrosopumilus maritimus
1.14.99.50 evolution EgtB contains a strongly conserved HX3HXE motif, implying that it is a member of the facial triad enzyme family with the Fe(II) site ligated by 2-His-1-Glu Mycobacterium avium
1.14.99.52 malfunction mutation of any of the residues in the HX3HXE motif in OvoA results in an over 100fold attenuation of activity Erwinia tasmaniensis
1.14.99.52 additional information residues in the HX3HXE motif are catalytically important (i.e., likely bind iron). Structure homology modeling, overview Erwinia tasmaniensis