Information on EC 1.13.11.53 - acireductone dioxygenase (Ni2+-requiring)

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.13.11.53
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RECOMMENDED NAME
GeneOntology No.
acireductone dioxygenase (Ni2+-requiring)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + formate + CO
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dioxygenation
-
-
oxidation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3-methylthiopropanoate biosynthesis
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Cysteine and methionine metabolism
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Metabolic pathways
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SYSTEMATIC NAME
IUBMB Comments
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming)
Requires Ni2+. If iron(II) is bound instead of Ni2+, the reaction catalysed by EC 1.13.11.54, acireductone dioxygenase [iron(II)-requiring], occurs instead [1]. The enzyme from the bacterium Klebsiella oxytoca (formerly Klebsiella pneumoniae) ATCC strain 8724 is involved in the methionine salvage pathway.
CAS REGISTRY NUMBER
COMMENTARY hide
221681-64-7
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
subspecies Oryza sativa indica
SwissProt
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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either facilitates recycling of methionine in living cells or exits this recycling pathway. Ni2+-dependent ARD produces methylthiopropionate, CO, and formate
additional information
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upon splitting of dioxygen, the enzyme immediately decomposes the reacting system into its three experimentally found products. crystal structure analysis, structure modeling and molecular simulations of the Ni2+ and Fe2+ enzyme, cf. 1.13.11.54, QM-DMD domain, overview
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(1Z)-1,2-dihydroxyhex-1-en-3-one + O2
n-butanoic acid + formic acid + CO
show the reaction diagram
1,2-dihydroxy-3-keto-1-hexene + O2
?
show the reaction diagram
-
incorporation of O2 into C1 and C3 of 1,2-dihydroxy-3-keto-1-hexene
-
-
?
1,2-dihydroxy-3-oxo-3-phenyl-1-propene + O2
?
show the reaction diagram
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-
-
-
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)-2-oxobutanoate + formate
show the reaction diagram
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-
-
-
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
show the reaction diagram
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
4-methylthio-2-ketobutyrate + formate + CO
show the reaction diagram
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-
-
?
1,2-dihydroxyhex-1-en-3-one + O2
butyrate + formate + CO
show the reaction diagram
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-
-
-
?
1-phosphonooxy-2,2-dihydroxy-3-oxo-3-phenylpropane + O2
?
show the reaction diagram
part of the Met salvage pathway
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-
?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)-2-oxobutanoate + formate
show the reaction diagram
-
-
-
-
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
show the reaction diagram
additional information
?
-
-
it is proposed that Rnt1p cleavage and/or degradation by exonucleases helps prevent the accumulation of ADI1 mRNA prior to heat shock conditions. The ribonucleolytic pathways provide a mechanism to eliminate 3'-extended forms that arise from poor 3'-end processing signals present at the end of the ADI1 gene
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
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the Fe2+ bound protein catalyzes the reaction of EC 1.13.11.54
Mg2+
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required
Nickel
Zn2+
Zn2+-form of enzyme, less than 1 mol per mol of protein
additional information
-
the identity of bound metal ion does not affect the oligomeric state of ARD
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cycloheximide
0.0711 mM or higher
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0493 - 0.2871
(1Z)-1,2-dihydroxyhex-1-en-3-one
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0.05
1,2-dihydroxy-3-keto-1-hexene
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-
0.044 - 500
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one
0.0392
1-phosphonooxy-2,2-dihydroxy-3-oxo-3-phenylpropane
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0.11 - 500
O2
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7.87 - 17.1
(1Z)-1,2-dihydroxyhex-1-en-3-one
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500
1,2-dihydroxy-3-keto-1-hexene
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
60 - 160
(1Z)-1,2-dihydroxyhex-1-en-3-one
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.3
calculated value
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
18500
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1 * 18500, SDS-PAGE
20000
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1 * 20000, SDS-PAGE
20250
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mass spectrometry
21391
1 * 21391
23000 - 26000
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gel filtration
23700
Western blot
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis
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quantum-classical dynamics simulations with Co2+ bound. Both Fe2+-like (reaction of EC 1.13.11.54) and Ni2+-like (reaction of EC 1.13.11.53) routes are accessible to Co2+-ARD. with low spin Co2+, the reaction exclusively follows the Fe2+-dependent pathways, producing alpha-keto acid precursor of methionine and formate, while the high spin Co2+ path contains a bifurcation in the pathway that follows along both the Fe2+-dependent pathway and Ni2+-dependent pathway that produces methylthiopropionate, carbon monoxide and formate
nanodroplet vapour diffusion method using 19.0% (w/v) polyethylene glycol 4000, 19.0% (w/v) isopropanol, 5.0% glycerol, and 0.095 M Na-citrate pH 4.2 (final pH 5.6)
Ni- and Co-bound proteins. Both Ni and Co present an octahedral coordination geometry in the active site bound to protein ligands H88, H90, H133 and E94. Additionally, two distinct water (or hydroxide) ligands bind to the metal ion center
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
43
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Mn2+ bound enzyme, melting temperature
58
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Ni2+ bound enzyme, melting temperature
additional information
Ni2+-bound ARD is the most stable followed by Co2+ and Fe2+, and Mn2+-bound ARD being the least stable
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DEAE cellulose column chromatography and Phenyl-Sepharose column chromatography
Superdex 200 column chromatography and nickel-chelating resin column chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli BL21 cells
expressed in Escherichia coli strain BL21(DE3)pLysS
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expression in Escherichia coli
overexpression in HEK-293 cell
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E94A
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no activity
D101A
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about 60% of wild-type activity
E100A
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about 2% of wild-type activity. E100 is not essential for metal binding
E102A
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no catalytic activity
E95A
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about 4% of wild-type activity
H140A
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no catalytic activity
H140F
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no catalytic activity
H96A
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no catalytic activity
H98A
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no catalytic activity
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
unfolded using 8 mM urea and refolded in the presence of 20 mM Ni2+
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
detection of one-bond 15N-13Calpha correlations in the vicinity of the paramagnetic Ni2+ via a double-quantum correlation experiment
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