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Information on EC 1.13.11.53 - acireductone dioxygenase (Ni2+-requiring)
for references in articles please use BRENDA:EC1.13.11.53
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EC Tree 1 Oxidoreductases
1.13 Acting on single donors with incorporation of molecular oxygen (oxygenases)
1.13.11 With incorporation of two atoms of oxygen
1.13.11.53 acireductone dioxygenase (Ni2+-requiring)
IUBMB Comments
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 . The enzyme from the bacterium Klebsiella oxytoca (formerly Klebsiella pneumoniae) ATCC strain 8724 is involved in the methionine salvage pathway.
The enzyme appears in viruses and cellular organisms
- 1.13.11.53
-
salvage
- monoxide
-
cupins
- mta
-
on-pathway
- oxytoca
-
nickel-containing
-
ketoacid
-
ni2+-containing
-
membrane-type
-
submergence-induced
-
nickel-dependent
-
nickelii
- nife-hydrogenase
- benzil
- 2-keto-4-methylthiobutyrate
- ch3cn
-
metallocenters
- analysis
Reaction Schemes
showSynonyms
acireductone dioxygenase, aci-reductone dioxygenase, ni-ard, acireductone dioxygenase 1, sip-l, human aci-reductone dioxygenase 1, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
acidoreductone dioxygenase
ADI1
ARD
membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1
-
MTCBP-1
Ni-ARD
nickel acireductone dioxygenase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 3-(methylsulfanyl)propanoate + formate + CO
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
oxidation
-
ARD (Ni) converts aci-reductone to 3-(methylthio)propanoate, carbon monoxide, and formate, and the reaction is not part of the methionine salvage pathway cycle (off-pathway).
oxidation
-
if Ni+2 is bound in the active site, the substrate acireductone reacts with O2 to yield formate and 4-methylthio-2-ketobutyrate
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PATHWAY SOURCE
PATHWAYS
MetaCyc
3-methylthiopropanoate biosynthesis
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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.
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CAS REGISTRY NUMBER
COMMENTARY
221681-64-7
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
1,2-dihydroxy-3-keto-1-hexene + O2
?
-
Substrates: incorporation of O2 into C1 and C3 of 1,2-dihydroxy-3-keto-1-hexene
Products: -
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?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
4-(methylsulfanyl)-2-oxobutanoate + formate
Substrates: -
Products: -
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?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
4-(methylthio)-2-oxobutanoate + formate
-
Substrates: -
Products: -
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?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
4-methylthio-2-ketobutyrate + formate
-
Substrates: -
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?
1,2-dihydroxyhex-1-en-3-one + O2
butyrate + formate + CO
-
Substrates: -
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?
1-phosphonooxy-2,2-dihydroxy-3-oxo-3-phenylpropane + O2
?
Substrates: part of the Met salvage pathway
Products: -
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?
2-hydroxy-3-oxo-1,3-diphenylprop-1-en-1-olate + O2
?
-
Substrates: -
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(1Z)-1,2-dihydroxyhex-1-en-3-one + O2
n-butanoic acid + formic acid + CO
Substrates: i.e. desthio-acireductone
Products: -
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?
(1Z)-1,2-dihydroxyhex-1-en-3-one + O2
n-butanoic acid + formic acid + CO
-
Substrates: i.e. desthio-acireductone
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1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
Substrates: -
Products: -
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?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
Substrates: -
Products: -
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?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
Substrates: -
Products: -
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?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
ir
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: enzyme of the methionine salvage pathway
Products: -
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1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: reaction is a shunt out of the methionine salvage pathway
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1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: the enzyme represents a branch point in the methionine salvage pathway leading from methylthioadenosine to methionine
Products: -
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?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: Ni2+ or Co2+ bound to the enzyme protein. If Fe2+ is bound instead of Ni2+ reaction catalyzed by EC 1.13.11.54 occurs instead
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1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: ordered-sequential mechanism
Products: -
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?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
Substrates: -
Products: -
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?
additional information
?
-
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Substrates: support Hepatitis C virus infection by enhance of cell uptake and replication of Hepatitis C virus
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additional information
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Substrates: human ARD is capable of metal-dependent dual chemistry. The Fe2+-bound ARD shows the highest activity and catalyzes on-pathway chemistry, i.e. reaction of EC 1.13.11.54, whereas Ni2+, Co2+ or Mn2+ forms catalyze off-pathway chemistry, i.e. reasctions of EC 1.13.11.53. The enzymatic activity is metal ion cofactor dependent and the activity trend in decreasing order is Fe2+ > Ni2+ = Co2+ > Mn2+
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additional information
?
-
-
Substrates: human ARD is capable of metal-dependent dual chemistry. The Fe2+-bound ARD shows the highest activity and catalyzes on-pathway chemistry, i.e. reaction of EC 1.13.11.54, whereas Ni2+, Co2+ or Mn2+ forms catalyze off-pathway chemistry, i.e. reasctions of EC 1.13.11.53. The enzymatic activity is metal ion cofactor dependent and the activity trend in decreasing order is Fe2+ > Ni2+ = Co2+ > Mn2+
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additional information
?
-
-
Substrates: aliphatic carbon-carbon bond cleavage reactivity of a mononuclear Ni(II) cis-beta-keto-enolate complex in the presence of base and O2: a model reaction for acireductone dioxygenase
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additional information
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Substrates: paramagnetic nickel(II) complexes of macrocyclic N4 ligands are able to perform as enzyme-substrate mimic for the nickel containing acireductone dioxygenase enzyme
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additional information
?
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Substrates: Schiff-base nickel biomimetic model complexes exhibit carbon-carbon bond cleavage activation of lithium acetylacetonate
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additional information
?
-
Substrates: the nickel complex [NiII(OPhN4(6-H-DPEN)(H2O))] is a structural analogue for the resting state of the active site of the nickel oxygenase nickel acireductone dioxyegenase and capable of carbon-carbon bond cleavage of a ketone presumably via dioxygenase type chemistry in line with the reactivity of the enzyme
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additional information
?
-
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Substrates: 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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?
additional information
?
-
-
Substrates: a mononuclear NiII complex bearing the monoanion of 1-acetoxy-3-phenylpropane-2,3-dione as a ligand, i.e. (N,N-bis[(6-phenyl-2-pyridyl)methyl]-N-(2-pyridylmethyl)amine)Ni[PhC(O)C(O)CHOC(O)CH3]ClO4 after deprotection by the addition of NaOCH3 in methanol generates a NiII species that contains a coordinated dianionic C(1)-H acireductone. Exposure of this acireductone to O2 leads to regioselective oxidative cleavage reactivity akin to that found for the NiII-containing acireductone dioxygenase enzyme
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
4-(methylsulfanyl)-2-oxobutanoate + formate
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
4-(methylthio)-2-oxobutanoate + formate
-
Substrates: -
Products: -
Products: -
?
additional information
?
-
-
Substrates: 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
Products: -
Products: -
?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2
3-(methylsulfanyl)propanoate + formate + CO
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: -
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: enzyme of the methionine salvage pathway
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: reaction is a shunt out of the methionine salvage pathway
Products: -
Products: -
?
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2
3-(methylthio)propanoate + formate + CO
-
Substrates: the enzyme represents a branch point in the methionine salvage pathway leading from methylthioadenosine to methionine
Products: -
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Iron
the enzyme contains a non-heme, iron-binding site critical for its activity
Mn2+
Ni2+
Nickel
additional information
-
the identity of bound metal ion does not affect the oligomeric state of ARD
Co2+
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, but the mechanism involves a bifurcating transition state, and so the exact product distribution is determined by the reaction dynamics
Co2+
-
apoenzyme is catalytically inactive. Addition of Ni2+ or Co2+ yields activity. Production in intact Escherichia coli of E-2' depends on the availability of the Fe2+. Enzyme contains 1.1 Ni2+ per enzyme molecule
Co2+
-
Ni2+ bound ARD is the most stable followed by Co2+ and Fe2+, and Mn2+-bound ARD being the least stable
Mn2+
-
Ni2+ bound ARD is the most stable followed by Co2+ and Fe2+, and Mn2+-bound ARD being the least stable
Ni2+
-
apoenzyme is catalytically inactive. Addition of Ni2+ or Co2+ yields activity. Production in intact Escherichia coli of E-2' depends on the availability of the Fe2+. Enzyme contains 1.1 Ni2+ per enzyme molecule
Ni2+
-
solution structure of the nickel-containing enzyme is determined using NMR methods. X-ray absorption spectroscopy, assignment of hyperfine shifted NMR resonance and conserved domain homology are used to model the metal-binding site because of the paramagnetism of the bound Ni2+
Ni2+
-
structure of the Ni site in resting Ni-ARD as containing a six coordinate Ni site composed of O/N-donor ligands including 3-4 histidine residues. The substrate binds to the Ni center in a bidentate fashion by displacing two ligands, at least one of which is a histidine ligand
Ni2+
-
model for the solution structure of the paramagnetic Ni2+-containing enzyme
Ni2+
-
Ni2+ can be conservatively replaced by Mn2 +or Co2+, giving rise to ARD activity (CO production)
Ni2+
-
Ni2+ bound ARD is the most stable followed by Co2+ and Fe2+, and Mn2+-bound ARD being the least stable
Nickel
detection of one-bond 15N-13Calpha correlations in the vicinity of the paramagnetic Ni2+
Nickel
-
ligands are H96, H98, E102 and H140, the same as in the isoform requiring Fe2+, 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
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
about 9fold increased enzyme activity 26 h after wounding of the potatoe, increased gene expression at the wound surface of the potatoe tuber
-
additional information
-
about 9fold increased enzyme activity 26 h after wounding of the potatoe, increased gene expression at the wound surface of the potatoe tuber
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Carcinogenesis
Human acireductone dioxygenase (HsARD), cancer and human health: Black hat, white hat or gray?
Carcinoma
Human acireductone dioxygenase (HsARD), cancer and human health: Black hat, white hat or gray?
Carcinoma, Hepatocellular
Hepatitis C virus infection in mouse hepatoma cells co-expressing human CD81 and Sip-L.
Carcinoma, Hepatocellular
The methionine salvage pathway-involving ADI1 inhibits hepatoma growth by epigenetically altering genes expression via elevating S-adenosylmethionine.
Hepatitis C
dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers.
Hepatitis C
Emergence of mutation clusters in the HCV genome during sequential viral passages in Sip-L expressing cells.
Hepatitis C
Hepatitis C virus infection in mouse hepatoma cells co-expressing human CD81 and Sip-L.
Hepatitis C
Interaction between hepatic membrane type 1 matrix metalloproteinase and acireductone dioxygenase 1 regulates hepatitis C virus infection.
Hepatitis C
Membrane-type 1 matrix metalloproteinase cytoplasmic tail-binding protein-1 is a new member of the Cupin superfamily. A possible multifunctional protein acting as an invasion suppressor down-regulated in tumors.
Infections
Hepatitis C virus infection in mouse hepatoma cells co-expressing human CD81 and Sip-L.
Neoplasms
Human acireductone dioxygenase (HsARD), cancer and human health: Black hat, white hat or gray?
Neoplasms
The methionine salvage pathway-involving ADI1 inhibits hepatoma growth by epigenetically altering genes expression via elevating S-adenosylmethionine.
Prostatic Neoplasms
Expression and function of the human androgen-responsive gene ADI1 in prostate cancer.
Prostatic Neoplasms
The methionine salvage pathway-involving ADI1 inhibits hepatoma growth by epigenetically altering genes expression via elevating S-adenosylmethionine.
Virus Diseases
dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers.
Virus Diseases
Hepatitis C virus infection in mouse hepatoma cells co-expressing human CD81 and Sip-L.
Virus Diseases
Interaction between hepatic membrane type 1 matrix metalloproteinase and acireductone dioxygenase 1 regulates hepatitis C virus infection.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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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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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
additional information
-
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
physiological function
-
either facilitates recycling of methionine in living cells or exits this recycling pathway. Ni2+-dependent ARD produces methylthiopropionate, CO, and formate
physiological function
enzyme expression promotes 5'-methylthioadenosine cycle to increase S-adenosylmethionine levels, which alter genome-wide promoter methylation profiles, resulting in altered gene expression and hepatocellular carcinoma growth suppression
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Bacillus anthracis str. 'Ames Ancestor
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E94A
H133A
the mutation at the metal-binding site abolishes both functions of the enzyme in cell growth inhibition and apoptosis enhancement
E100A
-
about 2% of wild-type activity. E100 is not essential for metal binding
H98S
E94A
the mutant has an increased percentage of apoptotic cells similar to those expressing wild type enzyme
H98S
-
no catalytic activity. Mutant exhibits little affinity for either Ni2+ or Fe2+, indicating that His 98 is likely involved in binding both metals
H98S
-
mutation results in the formation of a stable soluble protein that while structurally different from ARD-Ni+2 shows a high degree of similarity to the ARD'(Fe) enzyme
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TEMPERATURE STABILITY
ORGANISM