Information on EC 1.13.11.54 - acireductone dioxygenase [iron(II)-requiring]

for references in articles please use BRENDA:EC1.13.11.54
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.13.11.54
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RECOMMENDED NAME
GeneOntology No.
acireductone dioxygenase [iron(II)-requiring]
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 4-(methylthio)-2-oxobutanoate + formate
show the reaction diagram
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation
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methionine metabolism
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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-forming)
Requires iron(II). If Ni2+ is bound instead of iron(II), the reaction catalysed by EC 1.13.11.53, acireductone dioxygenase (Ni2+-requiring), occurs instead. 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
221681-63-6
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221681-64-7
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
indica cultivar Pin Gaew 56
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
additional information
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
2-oxovalerate + formic acid
show the reaction diagram
1,2-dihydroxy-3-oxopent-1-ene + O2
2-oxo-butanoate + formate
show the reaction diagram
-
-
-
-
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
2-keto-4-methyl thiobutyrate + formate
show the reaction diagram
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + 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
-
-
-
-
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
4-(methylthio)-2-oxobutanoate + formate
show the reaction diagram
1,2-dihydroxyhex-1-en-3-one + O2
2-oxopentanoate + formate
show the reaction diagram
-
incorporation of O2 into C1 and C2 of 1,2-dihydroxy-3-keto-1-hexene
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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)propanoate + formate + CO
show the reaction diagram
-
-
-
-
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
4-(methylthio)-2-oxobutanoate + formate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe
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enzyme contains 1 atom of Fe
Iron
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ligands are H96, H98, E102 and H140, the same as in the isoform requiring Ni2+, EC 1.13.11.54. Structural and functional differences between FeARD' and NiARD' forms are triggered by subtle differences in the local backbone. Both enzymes bind their respective metals with pseudo-octahedral geometry and both may lose a His ligand upon binding of substrate under anaerobic conditions
Mn2+
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the Ni2+ bound protein catalyzes the reaction of EC 1.13.11.53
Ni2+
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the Ni2+ bound protein catalyzes the reaction of EC 1.13.11.53
additional information
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the identity of bound metal ion does not affect the oligomeric state of ARD
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Arabidopsis thaliana G protein beta
possible mechanism for Arabidopsis thaliana G protein beta activation of acireductone dioxygenase 1 activity, overview
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1185
(1Z)-1,2-dihydroxyhex-1-en-3-one
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Fe2+ bound enzyme, pH 7.0, 25°C
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25.9
1,2-dihydroxy-3-oxopent-1-ene
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210
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one
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0.052
1,2-dihydroxyhex-1-en-3-one
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0.047 - 210
O2
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
111.7
(1Z)-1,2-dihydroxyhex-1-en-3-one
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Fe2+ bound enzyme, pH 7.0, 25°C
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11.7
1,2-dihydroxy-3-oxopent-1-ene
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-
260
1,2-dihydroxyhex-1-en-3-one
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11.8 - 260
O2
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
950
(1Z)-1,2-dihydroxyhex-1-en-3-one
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Fe2+ bound enzyme, pH 7.0, 25°C
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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strongly induced in adventitious roots and in the youngest internode of partially submerged plants
Manually annotated by BRENDA team
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strongly induced in adventitious roots and in the youngest internode of partially submerged plants
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20000
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1 * 20000, SDS-PAGE
23000 - 26000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
additional information
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
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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
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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
recombinant
recombinant His-tagged acireductone dioxygenase 1 and GST-tagged acireductone dioxygenase 1 by nickel affinity and glutathione affinity chromatographies, respectively
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli strain BL21(DE3)pLysS
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expression in Escherichia coli
transient expression of GFP-acireductone dioxygenase 1 in Arabidopsis thaliana protoplasts. The coding regions of ARD1–4 are cloned into pDEST17TM and pDEST15TM containing an N-terminal poly-His tag and an N-terminal GST tag, respectively, and are expressed in Escherichia coli strain Rosetta BL21
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
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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matrix metalloproteinase MT1-MMP physically interacts with claudin-1 and acireductone dioxygenase 1, both associated with hepatitis C virus cell entry. Positive cytoplasmic ADI1 in liver biopsies is associated with higher serum hepatitis C virus RNA levels. Positive MT1-MMP and ADI1 interaction is associated with lower tissue hepatitis C virus RNA levels. Hepatic hepatitis C virus RNA levels are positively associated with ADI1 levels in the MT1-MMP and ADI1 coimmunoprecipitates
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