GO:0010308 acireductone dioxygenase (Ni2+-requiring) activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0010308 describes a nickel-dependent dioxygenase that converts 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one (acireductone) and O2 into 3-(methylthio)propanoate, carbon monoxide, and formate.
• The same protein scaffold can bind either Ni2+ or Fe2+, and the identity of the metal dictates whether the enzyme produces CO and formate (Ni-ARD) or a keto acid (Fe-ARD).
• Human acireductone dioxygenase (ADI1) is a non-heme metalloenzyme whose metal occupancy and structure have been studied by crystallography and computational modeling.
• ADI1 is regulated by cellular iron status through the iron chaperone PCBP1, with PCBP2 acting as a potential co-chaperone.
• The Ni2+-requiring activity is part of the methionine salvage pathway and polyamine metabolism, linking it to cancer, oxidative stress, and metabolic disease.
• Biomimetic Ni(II)N3O model complexes reproduce key aspects of Ni-ARD reactivity, providing mechanistic insight into O2 activation.
Description
Acireductone dioxygenase (Ni2+-requiring) activity, encoded by GO:0010308, is a molecular function defined by the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + CO + formate. This activity is catalyzed by acireductone dioxygenase (ARD), a non-heme metalloenzyme that can bind either nickel or iron, with the metal identity determining the reaction outcome. The nickel-bound form (Ni-ARD) is the one annotated under GO:0010308, while the iron-bound form (Fe-ARD) catalyzes a different oxidative cleavage. Researchers study this activity because it sits at the intersection of methionine salvage, polyamine metabolism, and cellular metal homeostasis. In humans, the ortholog ADI1 (acireductone dioxygenase 1) is implicated in these pathways and is regulated by iron availability. Understanding GO:0010308 therefore requires integrating enzymology, metal biochemistry, and cellular physiology.
acireductone dioxygenase (Ni2+-requiring) activity At A Glance
| GO ID | GO:0010308 |
|---|---|
| GO term | acireductone dioxygenase (Ni2+-requiring) activity |
| Ontology | molecular_function |
| Synonym | 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming); 2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase activity; acireductone dioxygenase activity; ARD activity; E-2 activity |
| Major function | Catalyzes the oxidative cleavage of acireductone to 3-(methylthio)propanoate, CO, and formate using Ni2+ as cofactor |
| Metal cofactor | Nickel (Ni2+); the enzyme can also bind Fe2+ but then catalyzes a different reaction |
| Pathway context | Methionine salvage and polyamine metabolism |
| Human gene | ADI1 (acireductone dioxygenase 1) |
What Is GO:0010308?
GO:0010308 is defined by the QuickGO as the catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + CO + formate. In simpler terms, it is a nickel-dependent dioxygenase activity that uses molecular oxygen to cleave acireductone into 3-(methylthio)propanoate, carbon monoxide, and formate. This activity is one of two possible reactions catalyzed by acireductone dioxygenase, the other being the iron-dependent formation of a keto acid.
Why Is acireductone dioxygenase (Ni2+-requiring) activity Important in Cell Biology?
GO:0010308 is important because it defines a metal-dependent branch point in cellular metabolism that influences methionine salvage, polyamine homeostasis, and redox balance. The nickel requirement distinguishes it from the iron-dependent activity of the same protein, making it a paradigm for how metal cofactors can switch enzyme chemistry. In humans, ADI1 is regulated by iron via PCBP1/PCBP2, linking this activity to iron metabolism and potentially to diseases of iron overload or deficiency. Understanding this activity also informs the design of nickel-dependent enzyme inhibitors and biomimetic catalysts.
• Defines a key step in the methionine salvage pathway, recycling sulfur from polyamines.
• Represents a classic example of metal-driven reaction specificity (Ni vs Fe).
• Links to polyamine metabolism, which is often dysregulated in cancer.
• Human ADI1 is regulated by iron chaperones PCBP1/PCBP2, connecting it to iron homeostasis.
• Nickel-dependent enzymes are important in microbial pathogenesis and biotechnology.
• Provides a target for mechanistic studies using model complexes.
• Relevant to understanding carbon monoxide production in biological systems.
• May influence oxidative stress responses through acireductone metabolism.
• Informs the development of enzyme inhibitors for metabolic diseases.
• Serves as a model for studying non-heme dioxygenases.
Molecular Mechanism of acireductone dioxygenase (Ni2+-requiring) activity
Substrate binding and metal coordination
In simple terms: The enzyme uses a nickel ion to grab the substrate and oxygen.
In Ni-ARD, the active site contains a Ni2+ ion coordinated by a His3Asp or similar N3O ligand set, as shown in structural and biomimetic studies. The substrate, 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one, binds to the metal, positioning it for oxidative attack.
Oxygen activation and oxidative cleavage
In simple terms: Oxygen is split and inserted into the substrate, breaking it apart.
Molecular oxygen binds to the nickel center and is activated, leading to cleavage of the substrate into 3-(methylthio)propanoate, CO, and formate. This reaction is distinct from the Fe-ARD reaction, which produces a keto acid instead.
Metal-dependent reaction partitioning
In simple terms: The metal in the enzyme decides which products are made.
The same protein can bind either Ni2+ or Fe2+, and the metal identity dictates whether the reaction follows the Ni-ARD pathway (CO and formate) or the Fe-ARD pathway (keto acid). This dual chemistry is a hallmark of acireductone dioxygenase.
Cellular regulation by iron chaperones
In simple terms: Cells control the enzyme by managing iron availability.
Human ADI1 is regulated by cellular iron through the iron chaperone PCBP1, with PCBP2 acting as a potential co-chaperone, affecting metal occupancy and activity.
Biomimetic models and mechanistic insight
In simple terms: Scientists build artificial versions to understand how the enzyme works.
A Ni(II)N3O structural model complex for the active site of Ni-ARD has been shown to mediate O2-dependent oxidation, providing biomimetic reactivity and enzymatic implications.
Key Genes Involved in GO:0010308 acireductone dioxygenase (Ni2+-requiring) activity
The following genes and proteins are directly or indirectly involved in acireductone dioxygenase (Ni2+-requiring) activity and its associated pathways.
| Gene | Major Role | Research Relevance |
|---|---|---|
| ADI1 | Human acireductone dioxygenase 1; catalyzes the Ni2+-dependent reaction | Studied for its role in methionine salvage and iron regulation |
| ARD | Bacterial acireductone dioxygenase; prototype for Ni/Fe dual chemistry | Model enzyme for metal-dependent catalysis |
| PCBP1 | Iron chaperone that regulates ADI1 metalation | Links iron homeostasis to ADI1 activity |
| PCBP2 | Potential co-chaperone for PCBP1 in ADI1 regulation | Modulates ADI1 function |
| MTR | Methionine synthase; part of methionine salvage | Context for ADI1 pathway |
| MTAP | Methylthioadenosine phosphorylase; upstream of acireductone | Polyamine/methionine salvage link |
| ENOPH1 | Enolase-phosphatase E1; produces acireductone | Substrate generation for ADI1 |
| SAMD1 | Methionine salvage pathway enzyme | Related to polyamine metabolism |
| ODC1 | Ornithine decarboxylase; polyamine synthesis | Upstream of methionine salvage |
| SAT1 | Spermidine/spermine N1-acetyltransferase | Polyamine catabolism |
| PAOX | Polyamine oxidase | Produces acireductone precursors |
| SMOX | Spermine oxidase | Polyamine catabolism |
| NME1 | Nucleoside diphosphate kinase; may interact with ADI1 | Potential regulatory link |
| NME2 | Nucleoside diphosphate kinase; may interact with ADI1 | Potential regulatory link |
| HIF1A | Hypoxia-inducible factor; may regulate ADI1 expression | Link to oxygen sensing |
| NCOA4 | Ferritinophagy receptor; affects iron availability | Indirect regulation of ADI1 |
| IREB2 | Iron-responsive element binding protein 2 | Iron-dependent regulation |
How Is acireductone dioxygenase (Ni2+-requiring) activity Regulated?
The activity of acireductone dioxygenase (Ni2+-requiring) is regulated at multiple levels. In humans, ADI1 is regulated by cellular iron status through the iron chaperone PCBP1, with PCBP2 acting as a potential co-chaperone, which affects metal occupancy and enzyme activity. The metal cofactor itself acts as a switch: nickel binding favors the GO:0010308 reaction, while iron binding leads to a different product profile. Additionally, expression of ADI1 may be influenced by hypoxia and iron-responsive elements, though direct evidence is still emerging.
acireductone dioxygenase (Ni2+-requiring) activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| ADI1 | Cancer (polyamine metabolism) | ADI1 knockout cancer cell lines; xenograft models |
| ADI1 | Iron metabolism disorders | ADI1 knockout cells with iron supplementation |
| PCBP1 | Iron overload | PCBP1 knockout or knockdown cells |
| ARD | Bacterial pathogenesis | Bacterial ARD mutants in infection models |
| ADI1 | Oxidative stress | ADI1 overexpression in neuronal cells |
Cancer and polyamine metabolism
Acireductone dioxygenase 1 (ADI1) is part of the methionine salvage pathway, which is closely tied to polyamine metabolism. Dysregulated polyamine metabolism is a hallmark of many cancers, and ADI1 expression has been linked to tumor progression in some studies. The Ni2+-requiring activity may influence cancer cell proliferation by affecting methionine availability and redox balance.
Iron metabolism disorders
ADI1 is regulated by the iron chaperone PCBP1, and disruptions in iron homeostasis can affect its activity. This links GO:0010308 to diseases of iron overload or deficiency, where altered ADI1 function may contribute to metabolic stress.
Neurodegeneration and oxidative stress
The methionine salvage pathway and polyamine metabolism are implicated in oxidative stress and neurodegeneration. Although direct evidence for ADI1 in neurodegeneration is limited, its role in maintaining methionine and glutathione levels suggests a potential contribution.
From acireductone dioxygenase (Ni2+-requiring) activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| What is the effect of ADI1 loss on methionine salvage? | ADI1 knockout cell lines (CRISPR) |
| How does metal substitution affect ADI1 activity? | Point mutations in metal-binding residues |
| Can ADI1 be tagged for localization studies? | Knock-in of fluorescent tag at ADI1 locus |
| Does ADI1 overexpression alter polyamine levels? | ADI1 overexpression cell lines |
| What is the role of PCBP1 in ADI1 regulation? | PCBP1 knockout or knockdown |
| Can Ni-ARD be modeled in vitro? | Recombinant ARD with Ni2+ reconstitution |
How to Study the acireductone dioxygenase (Ni2+-requiring) activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Enzymatic assay with HPLC | Substrate consumption and product formation | Kinetic characterization of Ni-ARD |
| ICP-MS | Metal content (Ni, Fe) | Metal occupancy of purified ADI1 |
| X-ray crystallography | Three-dimensional structure | Active site geometry of Ni-ARD |
| Site-directed mutagenesis | Effect of point mutations on activity | Identifying metal-binding residues |
| RNA-seq | Transcriptome changes | ADI1 knockout vs wild-type |
| Western blot | Protein expression and interaction | PCBP1-ADI1 regulation |
| Gas chromatography | CO production | Measuring Ni-ARD activity |
| Biomimetic synthesis | Model complex reactivity | Understanding O2 activation |
Enzymatic assays
The activity of Ni-ARD can be measured by monitoring the consumption of acireductone or the production of CO and formate using gas chromatography or mass spectrometry.
Structural biology
X-ray crystallography and NMR can determine the metal coordination and substrate binding in Ni-ARD, as demonstrated for human ADI1 and model complexes.
Metal analysis
Inductively coupled plasma mass spectrometry (ICP-MS) can quantify nickel and iron content in purified ADI1 to assess metal occupancy.
Gene expression and regulation
RNA-seq and qPCR can measure ADI1 mRNA levels under different iron conditions, while Western blot can assess protein levels and PCBP1 interaction.
How CRISPR Can Be Used to Study GO:0010308 acireductone dioxygenase (Ni2+-requiring) activity
Knockout
CRISPR knockout of ADI1 can abolish Ni2+-requiring acireductone dioxygenase activity, allowing researchers to study its role in methionine salvage and polyamine metabolism. Knockout cell lines can be used to assess sensitivity to oxidative stress and iron chelation.
Point Mutation
Point mutations in the metal-binding residues of ADI1 can switch metal preference or abolish activity, helping to dissect the Ni2+-specific reaction. For example, mutating histidine or aspartate ligands can alter nickel binding and catalysis.
Knock-in
Knock-in of a fluorescent tag (e.g., GFP) at the endogenous ADI1 locus enables real-time imaging of protein localization and dynamics without overexpression artifacts. This approach can also be used to introduce disease-associated mutations.
Overexpression
Overexpression of ADI1 in cell lines can amplify Ni2+-requiring activity, facilitating biochemical purification and structural studies. It can also be used to test whether increased activity affects polyamine levels and cell growth.
How EDITGENE Supports acireductone dioxygenase (Ni2+-requiring) activity Research
Researchers studying acireductone dioxygenase (Ni2+-requiring) activity-related genes often need to determine whether a candidate gene is causally involved in methionine salvage, polyamine metabolism, or metal homeostasis. EDITGENE provides comprehensive CRISPR-based services to generate precisely engineered cell models for such investigations.
Contact EDITGENE today to design your custom CRISPR model for acireductone dioxygenase (Ni2+-requiring) activity research.
Frequently Asked Questions About acireductone dioxygenase (Ni2+-requiring) activity
What is acireductone dioxygenase (Ni2+-requiring) activity?
It is a molecular function defined by GO:0010308, catalyzing the conversion of 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one and O2 to 3-(methylthio)propanoate, CO, and formate using nickel as a cofactor.
What genes are involved in acireductone dioxygenase (Ni2+-requiring) activity?
The primary gene is ADI1 in humans, and ARD in bacteria. Other related genes include PCBP1, PCBP2, and methionine salvage pathway enzymes.
What is the role of nickel in acireductone dioxygenase?
Nickel is required for the Ni-ARD reaction; it coordinates the substrate and activates oxygen, leading to CO and formate production.
How is acireductone dioxygenase regulated?
Human ADI1 is regulated by iron via the chaperone PCBP1, and metal availability determines whether the enzyme uses nickel or iron.
What diseases are associated with acireductone dioxygenase?
It is linked to cancer through polyamine metabolism and to iron metabolism disorders via PCBP1 regulation.
What is the difference between Ni-ARD and Fe-ARD?
Ni-ARD produces 3-(methylthio)propanoate, CO, and formate, while Fe-ARD produces a keto acid; the metal dictates the chemistry.
Can acireductone dioxygenase be studied with CRISPR?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are all used to study ADI1 function.
What methods measure acireductone dioxygenase activity?
Enzymatic assays with HPLC, gas chromatography for CO, and ICP-MS for metal content are commonly used.
Is acireductone dioxygenase a nickel enzyme?
Yes, the Ni2+-requiring form is a nickel-dependent enzyme, but the same protein can also bind iron.
What is the methionine salvage pathway?
It is a metabolic route that recycles sulfur from polyamines to methionine, and acireductone dioxygenase is a key enzyme in it.
Conclusion
GO:0010308 acireductone dioxygenase (Ni2+-requiring) activity represents a fascinating example of metal-dependent enzyme chemistry with broad implications for methionine salvage, polyamine metabolism, and iron homeostasis. The dual chemistry of acireductone dioxygenase, dictated by nickel versus iron, makes it a paradigm for studying metalloenzyme specificity. Human ADI1 is regulated by iron chaperones, linking this activity to cellular iron status and disease. Continued research using CRISPR models and biomimetic complexes will further illuminate its mechanistic and physiological roles.
References
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- 3. Deshpande AR et al.. 2017. Dual chemistry catalyzed by human acireductone dioxygenase.. Protein Eng Des Sel 30(3):197-204 PMID: 28062648
- 4. Deshpande AR et al.. 2017. The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase.. Chem Rev 117(15):10474-10501 PMID: 28731690
- 5. Bae DH et al.. 2018. The old and new biochemistry of polyamines.. Biochim Biophys Acta Gen Subj 1862(9):2053-2068 PMID: 29890242
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- 7. Bae DH et al.. 2020. Acireductone dioxygenase 1 (ADI1) is regulated by cellular iron by a mechanism involving the iron chaperone, PCBP1, with PCBP2 acting as a potential co-chaperone.. Biochim Biophys Acta Mol Basis Dis 1866(10):165844 PMID: 32480040
- 8. Kirsch KE et al.. 2024. Direct O(2) mediated oxidation of a Ni(II)N(3)O structural model complex for the active site of nickel acireductone dioxygenase (Ni-ARD): characterization, biomimetic reactivity, and enzymatic implications.. Dalton Trans 53(44):17852-17863 PMID: 39421893
