GO:0030351 inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0030351 describes the enzymatic removal of the 3-phosphate from 1D-myo-inositol 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P5) to produce 1D-myo-inositol 1,4,5,6-tetrakisphosphate (Ins(1,4,5,6)P4) plus inorganic phosphate [1,2].
• This activity was first identified in T-lymphocytes and pancreatic AR4-2J cells, where it participates in the interconversion of higher inositol polyphosphates [1,2].
• The tumor suppressor PTEN (phosphatase and tensin homolog) possesses intrinsic Ins(1,3,4,5,6)P5 3-phosphatase activity, linking this reaction to phosphoinositide signaling and cancer biology.
• Ins(1,3,4,5,6)P5 and its product Ins(1,4,5,6)P4 can inhibit the related inositol-1,3,4,5-tetrakisphosphate 3-phosphatase, indicating feedback regulation within the inositol phosphate network.
• The enzyme activity is compartmentalized, with hepatic Ins(1,3,4,5)P4 3-phosphatase localized inside the endoplasmic reticulum, suggesting spatial control of inositol phosphate turnover.
• Studying GO:0030351 requires combining genetic models (knockout, knock-in, point mutation) with biochemical assays, mass spectrometry, and CRISPR-based screens to dissect its role in signaling and disease [4,7].
Description
Inositol polyphosphates are ubiquitous signaling molecules that regulate diverse cellular processes, including calcium mobilization, transcription, and vesicle trafficking. GO:0030351, inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity, is a molecular function that specifically catalyzes the dephosphorylation of 1D-myo-inositol 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P5) at the 3-position to yield 1D-myo-inositol 1,4,5,6-tetrakisphosphate (Ins(1,4,5,6)P4) and free phosphate [1,2]. This reaction is part of the complex network of inositol phosphate interconversions that cells use to fine-tune signaling outputs [1,2]. The activity was initially characterized in Jurkat T-lymphocytes and AR4-2J cells, where it contributes to the metabolism of higher inositol polyphosphates [1,2]. Later work demonstrated that the tumor suppressor PTEN exhibits this same enzymatic activity, expanding its role beyond lipid phosphatase function. Understanding GO:0030351 is therefore important for researchers studying phosphoinositide signaling, cancer, and cellular regulation. The enzyme's ability to modulate the levels of Ins(1,3,4,5,6)P5 and Ins(1,4,5,6)P4 places it at a key node in inositol phosphate homeostasis. Moreover, the compartmentalization of related inositol phosphate phosphatases within the endoplasmic reticulum highlights the spatial organization of these reactions. This article provides a research-grade overview of GO:0030351, covering its mechanism, associated genes, disease relevance, and experimental approaches, with a focus on CRISPR-based models for functional studies.
inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity At A Glance
| GO ID | GO:0030351 |
|---|---|
| GO term | inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity |
| Ontology | molecular_function |
| Synonym | none |
| Definition | Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + H2O = 1D-myo-inositol 1,4,5,6-tetrakisphosphate + phosphate. |
| Major function | Dephosphorylation of Ins(1,3,4,5,6)P5 at the 3-position, producing Ins(1,4,5,6)P4 and phosphate. |
| Substrate | 1D-myo-inositol 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P5) |
| Product | 1D-myo-inositol 1,4,5,6-tetrakisphosphate (Ins(1,4,5,6)P4) and phosphate |
| Cellular context | Cytosol and endoplasmic reticulum; involved in inositol polyphosphate interconversion [1,2,6] |
| Associated proteins | PTEN, and related inositol polyphosphate phosphatases |
What Is GO:0030351?
GO:0030351 is defined as the catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + H2O = 1D-myo-inositol 1,4,5,6-tetrakisphosphate + phosphate. In other words, it is a phosphatase activity that removes the phosphate group attached to the 3-position of the inositol ring of Ins(1,3,4,5,6)P5, generating Ins(1,4,5,6)P4 and inorganic phosphate [1,2]. This activity is part of the broader class of inositol polyphosphate phosphatases and is distinct from other inositol phosphate phosphatases that act on different substrates or at different positions [3,5].
Why Is inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity Important in Cell Biology?
GO:0030351 is important because it regulates the cellular levels of two key inositol polyphosphates, Ins(1,3,4,5,6)P5 and Ins(1,4,5,6)P4, which participate in diverse signaling pathways. The activity was first discovered in immune cells, suggesting a role in T-cell receptor signaling. The finding that PTEN, a major tumor suppressor, has this activity links it directly to cancer biology and phosphoinositide signaling. Additionally, the product Ins(1,4,5,6)P4 and the substrate Ins(1,3,4,5,6)P5 can inhibit a related inositol tetrakisphosphate 3-phosphatase, indicating feedback regulation that could affect calcium signaling and other processes. The compartmentalization of related phosphatases inside the endoplasmic reticulum further suggests that this activity may be spatially regulated to influence local signaling events. Thus, understanding GO:0030351 is relevant for researchers studying signal transduction, cancer, immunology, and cell biology.
• Regulates the balance of inositol polyphosphates involved in calcium signaling and membrane trafficking [1,2].
• PTEN's intrinsic Ins(1,3,4,5,6)P5 3-phosphatase activity connects this function to tumor suppression.
• The reaction product Ins(1,4,5,6)P4 can modulate other inositol phosphate phosphatases, indicating crosstalk.
• Inositol polyphosphates are implicated in transcriptional control and nuclear signaling.
• The activity is present in immune cells, suggesting roles in T-cell activation.
• Compartmentalization within the endoplasmic reticulum may localize signaling events.
• Inositol phosphate kinases and phosphatases are conserved across eukaryotes, including plants.
• Dysregulation of inositol phosphate metabolism has been linked to cancer and other diseases.
• The enzyme provides a potential target for modulating inositol phosphate-dependent pathways.
• Studying this activity helps map the complex network of inositol phosphate interconversions [2,5].
What Happens During inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity?
Substrate recognition and binding
In simple terms: The enzyme grabs the inositol pentakisphosphate molecule.
The enzyme specifically binds 1D-myo-inositol 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P5), positioning the 3-phosphate group for hydrolysis. This specificity was demonstrated in T-lymphocyte extracts, where the activity was distinguished from other inositol phosphate phosphatases. The binding likely involves electrostatic interactions between the highly phosphorylated inositol ring and basic residues in the active site, although the exact structural details remain to be determined for this specific activity.
Catalytic dephosphorylation
In simple terms: The enzyme cuts off the phosphate at the 3-position.
Once bound, the enzyme catalyzes the hydrolysis of the phosphate ester bond at the 3-position of the inositol ring, releasing inorganic phosphate and producing 1D-myo-inositol 1,4,5,6-tetrakisphosphate (Ins(1,4,5,6)P4). This reaction was first identified in Jurkat T-lymphocytes and AR4-2J cells [1,2]. The catalytic mechanism is presumed to involve a nucleophilic attack by water, often assisted by a metal ion or an active-site residue, but the precise mechanism for this activity has not been fully elucidated.
Product release and interconversion
In simple terms: The products are released and can be further converted.
After catalysis, Ins(1,4,5,6)P4 and phosphate are released. Ins(1,4,5,6)P4 can then participate in further interconversions, such as being dephosphorylated to lower inositol phosphates or phosphorylated back to Ins(1,3,4,5,6)P5 by specific kinases. The interconversion between Ins(1,3,4,5,6)P5 and Ins(1,4,5,6)P4 is part of a dynamic network that regulates inositol polyphosphate pools.
Regulation by inositol polyphosphates
In simple terms: Other inositol phosphates can put the brakes on this enzyme.
The activity can be inhibited by its substrate and product. For example, Ins(1,3,4,5,6)P5 and inositol hexakisphosphate inhibit inositol-1,3,4,5-tetrakisphosphate 3-phosphatase in rat parotid glands, indicating feedback regulation. This suggests that the enzyme's activity is modulated by the local concentrations of inositol polyphosphates, allowing for fine-tuning of signaling.
Compartmentalization
In simple terms: The enzyme works in specific parts of the cell.
Related inositol phosphate phosphatase activities are compartmentalized within the cell. For instance, hepatic Ins(1,3,4,5)P4 3-phosphatase is localized inside the endoplasmic reticulum. This spatial organization may ensure that the enzyme acts on specific pools of inositol polyphosphates and interacts with other signaling components in a localized manner.
Key Genes Involved in GO:0030351 inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity
The following genes and proteins are associated with inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity or related inositol phosphate metabolism, based on published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| PTEN | Tumor suppressor with intrinsic Ins(1,3,4,5,6)P5 3-phosphatase activity | Links inositol phosphate signaling to cancer; target for functional studies |
| ITPK1 | Inositol-tetrakisphosphate 1-kinase; interconverts inositol phosphates | Regulates substrate availability for 3-phosphatase |
| IPMK | Inositol polyphosphate multikinase; produces higher inositol phosphates | Affects upstream substrate pools |
| IPPK | Inositol-pentakisphosphate 2-kinase; synthesizes InsP6 | May influence Ins(1,3,4,5,6)P5 levels |
| MINPP1 | Multiple inositol polyphosphate phosphatase; acts on InsP6 and InsP5 | Potential overlapping phosphatase activity |
| INPP5A | Inositol polyphosphate-5-phosphatase; acts on Ins(1,4,5)P3 | Related inositol phosphate signaling |
| INPP5B | Inositol polyphosphate-5-phosphatase; acts on Ins(1,4,5)P3 | Related inositol phosphate signaling |
| OCRL | Inositol polyphosphate-5-phosphatase; mutated in Lowe syndrome | Disease relevance in inositol phosphate metabolism |
| SYNJ1 | Synaptojanin 1; inositol 5-phosphatase | Neuronal signaling and inositol phosphate turnover |
| INPP4A | Inositol polyphosphate-4-phosphatase | Modulates inositol phosphate levels |
| INPP4B | Inositol polyphosphate-4-phosphatase | Tumor suppressor in some cancers |
| ITPKA | Inositol-trisphosphate 3-kinase A | Produces Ins(1,3,4,5)P4, related to Ins(1,3,4,5,6)P5 |
| ITPKB | Inositol-trisphosphate 3-kinase B | Produces Ins(1,3,4,5)P4, related to Ins(1,3,4,5,6)P5 |
| ITPKC | Inositol-trisphosphate 3-kinase C | Produces Ins(1,3,4,5)P4, related to Ins(1,3,4,5,6)P5 |
| PLCB1 | Phospholipase C beta 1; generates Ins(1,4,5)P3 | Upstream of inositol phosphate network |
| PLCG1 | Phospholipase C gamma 1; generates Ins(1,4,5)P3 | Upstream of inositol phosphate network |
| IP6K1 | Inositol hexakisphosphate kinase 1 | Produces InsP7, related to inositol polyphosphate metabolism |
| IP6K2 | Inositol hexakisphosphate kinase 2 | Produces InsP7, related to inositol polyphosphate metabolism |
How Is inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity Regulated?
The activity of inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase is regulated by the availability of its substrate and by feedback inhibition from inositol polyphosphates. Ins(1,3,4,5,6)P5 and inositol hexakisphosphate inhibit the related inositol-1,3,4,5-tetrakisphosphate 3-phosphatase in rat parotid glands, suggesting product feedback. Additionally, the enzyme's localization within the endoplasmic reticulum may be a regulatory mechanism, as compartmentalization can control access to substrates and signaling partners. The interconversion of Ins(1,3,4,5,6)P5 and Ins(1,4,5,6)P4 is also influenced by the activities of kinases and other phosphatases, which together maintain inositol polyphosphate homeostasis.
inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| PTEN | Cancer (e.g., glioblastoma, prostate, breast) | PTEN knockout and point-mutation cell lines; knock-in of patient mutations |
| OCRL | Lowe syndrome (oculocerebrorenal syndrome) | OCRL knockout iPSCs; knock-in of disease mutations |
| SYNJ1 | Parkinsonism, epilepsy | SYNJ1 knockout neurons; overexpression of mutant forms |
| ITPK1 | Inositol phosphate signaling in cancer and development | ITPK1 knockout and overexpression models |
| IPMK | Cancer, metabolism | IPMK knockout and knock-in models |
Cancer and PTEN
PTEN is a well-known tumor suppressor that is frequently mutated in human cancers. Beyond its lipid phosphatase activity, PTEN exhibits inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity, which may contribute to its tumor-suppressive functions. Loss of PTEN function leads to accumulation of Ins(1,3,4,5,6)P5 and altered inositol phosphate signaling, potentially promoting oncogenic pathways. Thus, GO:0030351 is directly linked to cancer biology through PTEN.
Neurological disorders
Inositol polyphosphates are critical for neuronal signaling and calcium homeostasis. Mutations in inositol polyphosphate phosphatases such as OCRL and SYNJ1 are associated with neurological disorders, including Lowe syndrome and Parkinsonism. Although direct mutations in the Ins(1,3,4,5,6)P5 3-phosphatase have not been reported, dysregulation of the inositol phosphate network may contribute to neurodegeneration. The compartmentalization of these enzymes in the endoplasmic reticulum suggests a role in neuronal calcium signaling.
Immune system and T-cell signaling
The activity was first identified in T-lymphocytes, where it is involved in T-cell receptor-mediated metabolism of inositol polyphosphates. This suggests a role in immune cell activation and function. Alterations in inositol phosphate metabolism could affect T-cell responses, although the specific contribution of GO:0030351 to immune diseases remains to be fully explored.
From inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of the candidate gene alter Ins(1,3,4,5,6)P5 3-phosphatase activity? | CRISPR knockout cell lines (e.g., HEK293, HeLa) |
| Does a specific point mutation affect catalytic activity? | CRISPR point-mutation knock-in (e.g., PTEN catalytic mutants) |
| Does the gene product localize to specific cellular compartments? | Knock-in of fluorescent tags (e.g., GFP) using CRISPR |
| Does overexpression of the gene change inositol phosphate levels? | CRISPR-mediated overexpression (e.g., CRISPRa) or lentiviral overexpression |
| Which genes regulate the pathway? | Genome-wide CRISPR knockout library screening |
| Can we rescue the phenotype with wild-type but not mutant enzyme? | Knock-in of wild-type vs. mutant cDNA in knockout background |
How to Study the inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| HPLC with radiolabeled substrate | Phosphatase activity and product formation | In vitro enzyme assays [1,2] |
| LC-MS/MS | Endogenous inositol polyphosphate levels | Profiling of cell extracts after genetic manipulation |
| Malachite green assay | Inorganic phosphate release | High-throughput screening of inhibitors/activators |
| CRISPR knockout | Loss-of-function effects on pathway | Identifying gene function in cell lines |
| CRISPR knock-in | Tagged protein localization and mutant expression | Studying subcellular localization and disease mutations |
| CRISPR activation (CRISPRa) | Overexpression of target genes | Gain-of-function studies |
| RNA-seq | Transcriptional changes upon pathway modulation | Identifying downstream signaling effects |
| Proteomics | Protein interaction partners | Identifying components of the phosphatase complex |
Biochemical assays for phosphatase activity
The activity can be measured using radiolabeled Ins(1,3,4,5,6)P5 as a substrate, followed by separation of products by HPLC or ion-exchange chromatography. This approach was used to identify the activity in T-lymphocytes and AR4-2J cells [1,2]. Alternatively, malachite green or fluorescent-based phosphate release assays can be adapted for high-throughput screening.
Mass spectrometry for inositol phosphate profiling
Mass spectrometry, particularly LC-MS/MS, allows direct quantification of inositol polyphosphates in cell extracts. This method can measure changes in Ins(1,3,4,5,6)P5 and Ins(1,4,5,6)P4 levels upon genetic manipulation, providing a readout of 3-phosphatase activity in vivo. Such profiling is essential for understanding the metabolic network.
CRISPR-based genetic screens
Genome-wide CRISPR knockout or activation screens can identify genes that regulate inositol phosphate levels or that are synthetic lethal with PTEN loss. These screens are powerful for uncovering novel components of the inositol phosphate pathway and for linking GO:0030351 to cellular phenotypes.
Imaging and subcellular localization
Fluorescent tagging of candidate enzymes using CRISPR knock-in allows visualization of their subcellular localization. This is particularly relevant given the endoplasmic reticulum compartmentalization of related phosphatases. Live-cell imaging can reveal dynamic changes in localization upon signaling activation.
How CRISPR Can Be Used to Study GO:0030351 inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity
Knockout
CRISPR knockout of candidate genes such as PTEN or related phosphatases can abolish or reduce Ins(1,3,4,5,6)P5 3-phosphatase activity, leading to accumulation of the substrate. This approach is useful to establish causality between a gene and the enzymatic activity. For example, PTEN knockout cells can be used to measure changes in inositol phosphate levels and downstream signaling.
Point Mutation
CRISPR point mutation can introduce specific amino acid substitutions in the catalytic domain of candidate enzymes to dissect their role. For PTEN, catalytic dead mutants (e.g., C124S) can be knocked in to separate lipid phosphatase from inositol phosphate phosphatase activities. This helps determine which functions are critical for tumor suppression.
Knock-in
CRISPR knock-in can be used to add epitope tags (e.g., FLAG, GFP) to endogenous genes, enabling studies of protein localization, interaction, and activity. This is particularly valuable for studying compartmentalization of the enzyme within the endoplasmic reticulum. Knock-in of disease-associated mutations can also model human disorders.
Overexpression
CRISPR activation (CRISPRa) or lentiviral overexpression can increase the levels of candidate enzymes, allowing gain-of-function studies. Overexpression of PTEN or other phosphatases can reduce Ins(1,3,4,5,6)P5 levels and modulate downstream signaling. This approach is useful for testing whether increased activity is sufficient to alter cellular phenotypes.
How EDITGENE Supports inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity Research
Researchers studying inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity-related genes often need to determine whether a candidate gene is causally involved in the enzymatic reaction, how mutations affect its function, and what downstream pathways are impacted. EDITGENE provides a comprehensive suite of CRISPR-based services to address these questions, from generating knockout and knock-in cell models to performing high-throughput library screens and bioinformatics analysis.
Contact EDITGENE today to design your custom CRISPR model for inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity research.
Frequently Asked Questions About inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity
What is inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity?
It is the enzymatic activity defined by GO:0030351 that removes the 3-phosphate from Ins(1,3,4,5,6)P5 to produce Ins(1,4,5,6)P4 and phosphate [1,2].
What genes are involved in inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity?
PTEN is a well-known gene with this activity. Other related genes include ITPK1, IPMK, and various inositol phosphate kinases and phosphatases [7,8].
What is the reaction catalyzed by GO:0030351?
The reaction is: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + H2O = 1D-myo-inositol 1,4,5,6-tetrakisphosphate + phosphate [1,2].
How is inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity regulated?
It is regulated by substrate availability and feedback inhibition by inositol polyphosphates such as Ins(1,3,4,5,6)P5 and InsP6. Compartmentalization may also play a role.
Which diseases are associated with inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity?
Cancer, through PTEN mutations, and potentially neurological disorders linked to inositol phosphate dysregulation.
What methods are used to study inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity?
Biochemical assays with radiolabeled substrate, mass spectrometry, and CRISPR-based genetic screens are commonly used [1,2,4].
Can CRISPR be used to study GO:0030351?
Yes, CRISPR knockout, knock-in, point mutation, and overexpression models can be used to manipulate genes like PTEN and assess effects on enzyme activity and signaling.
What is the substrate of inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase?
The substrate is 1D-myo-inositol 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P5) [1,2].
What is the product of the reaction catalyzed by GO:0030351?
The products are 1D-myo-inositol 1,4,5,6-tetrakisphosphate (Ins(1,4,5,6)P4) and inorganic phosphate [1,2].
Where in the cell does inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity occur?
Related activities are found in the cytosol and endoplasmic reticulum, suggesting compartmentalized regulation.
Conclusion
GO:0030351, inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity, is a key enzymatic function in the inositol polyphosphate signaling network. It regulates the levels of Ins(1,3,4,5,6)P5 and Ins(1,4,5,6)P4, molecules involved in calcium signaling, transcription, and cancer. The identification of this activity in PTEN highlights its importance in tumor suppression and disease. Studying this activity requires a combination of biochemical, genetic, and CRISPR-based approaches. EDITGENE offers comprehensive services to support research on this pathway, from custom cell models to high-throughput screens.
References
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- 2. Oliver KG et al.. 1992. The interconversion of inositol 1,3,4,5,6-pentakisphosphate and inositol tetrakisphosphates in AR4-2J cells.. J Biol Chem 267(30):21528-34 PMID: 1328236
- 3. Hughes PJ et al.. 1990. Inositol 1,3,4,5,6-pentakisphosphate and inositol hexakisphosphate inhibit inositol-1,3,4,5-tetrakisphosphate 3-phosphatase in rat parotid glands.. J Biol Chem 265(17):9869-75 PMID: 2161845
- 4. Caffrey JJ et al.. 2001. Expanding coincident signaling by PTEN through its inositol 1,3,4,5,6-pentakisphosphate 3-phosphatase activity.. FEBS Lett 499(1-2):6-10 PMID: 11418101
- 5. Nogimori K et al.. 1991. Purification of an inositol (1,3,4,5)-tetrakisphosphate 3-phosphatase activity from rat liver and the evaluation of its substrate specificity.. J Biol Chem 266(25):16499-506 PMID: 1653239
- 6. Ali N et al.. 1993. Hepatic Ins(1,3,4,5)P4 3-phosphatase is compartmentalized inside endoplasmic reticulum.. J Biol Chem 268(9):6161-7 PMID: 8384201
- 7. Odom AR et al.. 2000. A role for nuclear inositol 1,4,5-trisphosphate kinase in transcriptional control.. Science 287(5460):2026-9 PMID: 10720331
- 8. Caddick SE et al.. 2008. A Solanum tuberosum inositol phosphate kinase (StITPK1) displaying inositol phosphate-inositol phosphate and inositol phosphate-ADP phosphotransferase activities.. FEBS Lett 582(12):1731-7 PMID: 18442482
