NT5C2 (cytosolic purine 5'-nucleotidase, cN-II) is a cytosolic, Mg2+-dependent enzyme of the HAD (haloacid dehalogenase) superfamily that dephosphorylates 6-hydroxypurine nucleoside 5'-monophosphates. It acts preferentially on IMP and GMP, and also on their deoxy counterparts (dIMP, dGMP) and XMP, releasing the corresponding nucleoside (inosine, guanosine, xanthosine) and inorganic phosphate. In addition to this 5'-nucleotidase (phosphohydrolase) activity it possesses a nucleoside phosphotransferase activity, transferring a phosphate from a donor nucleoside monophosphate to an acceptor nucleoside (preferentially inosine, deoxyinosine, guanosine), so it is not a purely catabolic enzyme. The enzyme is an allosterically regulated homotetramer: it is activated by ATP, diadenosine polyphosphates and 2,3-bisphosphoglycerate and inhibited by inorganic phosphate, coupling its activity to the metabolic state of the cell. Through these activities cN-II controls intracellular purine (deoxy)nucleotide and nucleoside pools. It also dephosphorylates the active monophosphates of purine nucleoside-analog drugs, reversing their kinase-mediated activation; this contributes to resistance against purine-analog and thiopurine chemotherapy. Germline loss-of-function variants cause autosomal-recessive hereditary spastic paraplegia (SPG45/SPG65).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009154 purine ribonucleotide catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that NT5C2 participates in purine ribonucleotide catabolism. This is consistent with the enzyme's dephosphorylation of purine ribonucleotide monophosphates (IMP, GMP, XMP) to nucleosides, which is a catabolic step. Correct and captures a core biological role. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Broad specificity cytosolic 5'-nucleotidase that catalyzes file:human/NT5C2/NT5C2-uniprot.txt Has the highest activities for IMP |
| GO:0046037 GMP metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of a role in GMP metabolism. GMP is a preferred substrate of cN-II (dephosphorylated to guanosine). Well supported and redundant with the experimental IDA GMP-metabolic annotations below. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Has the highest activities for IMP and GMP |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that the enzyme is active in the cytosol. Matches the experimentally established cytosolic localization. Core location; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0008253 5'-nucleotidase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of 5'-nucleotidase activity. This is the core catalytic function of cN-II and is directly supported by multiple experimental annotations. Accept as representing a core molecular function. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Broad specificity cytosolic 5'-nucleotidase that catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates |
| GO:0046040 IMP metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of a role in IMP metabolism. IMP is the top substrate of cN-II. Well supported and redundant with the experimental IDA annotations. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Has the highest activities for IMP |
| GO:0050146 nucleoside phosphotransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of nucleoside phosphotransferase activity, a bona fide second catalytic activity of cN-II (it transfers phosphate from a donor NMP to an acceptor nucleoside). Directly supported by experimental IDA annotations. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt possesses a phosphotransferase activity by which it can transfer a phosphate from a donor nucleoside monophosphate to an |
| GO:0002953 5'-deoxynucleotidase activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: Rhea-based electronic mapping (RHEA:29379 dGMP, RHEA:29383 dIMP) to 5'-deoxynucleotidase activity. cN-II does dephosphorylate the deoxynucleotide monophosphates dIMP and dGMP, so this activity is real, but it is a lower-preference facet of the broad 5'-nucleotidase activity rather than a distinct core function. Keep as non-core. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Has the highest activities for IMP and GMP followed by dIMP, dGMP and XMP |
| GO:0005829 cytosol | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProt Subcellular Location keyword mapping. Correct cytosolic localization; redundant with the experimental IDA/IBA cytosol annotations. This is the gene's own correct core location, so accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0008253 5'-nucleotidase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Multi-method electronic annotation (ARBA / Rhea / EC 3.1.3.5) of the core 5'-nucleotidase activity. Redundant with the many experimental annotations of the same term. Correct core molecular function; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Broad specificity cytosolic 5'-nucleotidase that catalyzes |
| GO:0046054 dGMP metabolic process | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA machine-learning electronic annotation of dGMP metabolism. cN-II dephosphorylates dGMP, so this is correct; it is a lower-preference (deoxy) substrate. Redundant with the experimental IDA dGMP annotations. Keep as non-core relative to the IMP/GMP-centered core. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt followed by dIMP, dGMP and XMP |
| GO:0050146 nucleoside phosphotransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Multi-method electronic annotation (Rhea / EC 2.7.1.77) of nucleoside phosphotransferase activity, a bona fide catalytic activity of cN-II. Redundant with the experimental IDA annotations of the same term; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt possesses a phosphotransferase activity by which it can |
| GO:0005515 protein binding | IPI PMID:16189514 Towards a proteome-scale map of the human protein-protein in... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a large-scale yeast two-hybrid interactome screen (Rual et al. 2005). Uninformative about molecular function and not a core activity. Per policy, an IPI protein-binding annotation is not removed; mark as over-annotated. |
| GO:0005515 protein binding | IPI PMID:19060904 An empirical framework for binary interactome mapping. | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a high-throughput binary interactome mapping study. Uninformative; not a core function. Retain the IPI annotation but mark as over-annotated. |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a proteome-scale interactome map. Uninformative about molecular function; not core. Mark as over-annotated (IPI not removed). |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a proteome-scale interactome community study. Uninformative; not core. Mark as over-annotated. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a reference binary interactome map. Uninformative about function; not core. Mark as over-annotated. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a cell-specific interactome remodeling study. Uninformative; not core. Mark as over-annotated. |
| GO:0008253 5'-nucleotidase activity | EXP PMID:12907246 Cytosolic and mitochondrial deoxyribonucleotidases: activity... | ACCEPT | Summary: Experimental characterization of cN-II 5'-nucleotidase activity, including dephosphorylation of purine (deoxy)nucleotide analog monophosphates. Directly supports the core catalytic function. Accept. Supporting Evidence: PMID:12907246 Only cN-II showed some activity with the monophosphates of the two purine analogs |
| GO:0008253 5'-nucleotidase activity | EXP PMID:17405878 Crystal structure of human cytosolic 5'-nucleotidase II: ins... | ACCEPT | Summary: Experimental/structural study confirming that cN-II catalyzes dephosphorylation of 6-hydroxypurine nucleoside monophosphates. Supports the core 5'-nucleotidase activity. Accept. Supporting Evidence: PMID:17405878 Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates |
| GO:0005737 cytoplasm | IDA PMID:9371705 Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning a... | ACCEPT | Summary: Direct assay localizing the enzyme to the cytoplasm/cytosol. Consistent with the UniProt subcellular location. Correct core location; accept. (The more specific term cytosol is also annotated.) Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0050689 negative regulation of defense response to virus by host | IDA PMID:36159777 TRIM22 orchestrates the proliferation of GBMs and the benefi... | MARK AS OVER ANNOTATED | Summary: From a single glioblastoma study reporting that NT5C2 mediates K48-linked ubiquitination of the antiviral sensor RIG-I, thereby negatively regulating RIG-I/NF-kB signaling. This is a moonlighting claim well outside the enzyme's canonical purine-nucleotidase role, from one paper, and the study itself shows NT5C2 and RIG-I "interacted indirectly" (via TRIM22). It is an experimental IDA, so it is retained rather than removed, but flagged as a likely over-annotation needing independent confirmation. Supporting Evidence: PMID:36159777 NT5C2 is responsible for the K48-linked ubiquitination of RIG-I |
| GO:0061630 ubiquitin protein ligase activity | IDA PMID:36159777 TRIM22 orchestrates the proliferation of GBMs and the benefi... | MARK AS OVER ANNOTATED | Summary: Single-paper claim that NT5C2 acts as an E3-ubiquitin-ligase responsible for K48-linked ubiquitination of RIG-I in glioblastoma cells. NT5C2 is a HAD-fold metabolic phosphohydrolase with no recognizable ubiquitin-ligase (RING/HECT/RBR) domain, and the same study reports the NT5C2-RIG-I interaction is indirect. Retained as an experimental IDA (not removed) but marked as a likely over-annotation/moonlighting claim requiring independent validation; not a core molecular function. Supporting Evidence: PMID:36159777 NT5C2 is responsible for K48-linked ubiquitination |
| GO:0070936 protein K48-linked ubiquitination | IDA PMID:36159777 TRIM22 orchestrates the proliferation of GBMs and the benefi... | MARK AS OVER ANNOTATED | Summary: Companion process annotation to the ubiquitin-ligase claim from the same single glioblastoma study (K48-linked ubiquitination of RIG-I). Same caveats: outside the canonical function, single paper, indirect interaction. Retained as experimental IDA but marked over-annotated; not core. Supporting Evidence: PMID:36159777 NT5C2 is responsible for the K48-linked ubiquitination of RIG-I |
| GO:0005829 cytosol | IDA PMID:21873433 Suppression of 5'-nucleotidase enzymes promotes AMP-activate... | ACCEPT | Summary: Direct assay (cytoplasmic-fraction 5'-nucleotidase activity in human myotubes) supporting cytosolic localization. Correct core location; accept. Supporting Evidence: PMID:21873433 NT5C2 silencing decreased NT5 activity in the cytoplasmic fraction |
| GO:0006204 IMP catabolic process | IMP PMID:21873433 Suppression of 5'-nucleotidase enzymes promotes AMP-activate... | ACCEPT | Summary: siRNA silencing of NT5C2 in human myotubes altered nucleotide pools (increased AMP/ATP ratio), supporting a role in IMP catabolism (IMP -> inosine + Pi). This is a core catabolic process for cN-II. Accept. Supporting Evidence: PMID:21873433 Using siRNA to silence NT5C2 expression in cultured human myotubes, we observed a 2-fold increase in the AMP/ATP ratio |
| GO:0008253 5'-nucleotidase activity | IMP PMID:21873433 Suppression of 5'-nucleotidase enzymes promotes AMP-activate... | ACCEPT | Summary: NT5C2 knockdown reduced cytoplasmic 5'-nucleotidase activity, providing genetic evidence for the enzyme's 5'-nucleotidase activity. Supports the core molecular function; accept. Supporting Evidence: PMID:21873433 NT5C2 silencing decreased NT5 activity in the cytoplasmic fraction |
| GO:0008253 5'-nucleotidase activity | IDA PMID:9371705 Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning a... | ACCEPT | Summary: Recombinant enzyme shown to exhibit 5'-nucleotidase activity. Direct evidence for the core catalytic function. Accept. Supporting Evidence: PMID:9371705 It exhibited both 5'-nucleotidase and phosphotransferase activity |
| GO:0050146 nucleoside phosphotransferase activity | IDA PMID:9371705 Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning a... | ACCEPT | Summary: Recombinant enzyme shown to exhibit phosphotransferase activity. Direct evidence for the second bona fide catalytic activity (nucleoside phosphotransferase). Accept. Supporting Evidence: PMID:9371705 It exhibited both 5'-nucleotidase and phosphotransferase activity |
| GO:0008253 5'-nucleotidase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity transfer of 5'-nucleotidase activity from the rat ortholog (UniProtKB:D3ZMY7). Correct core molecular function, redundant with the direct experimental evidence. Accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Broad specificity cytosolic 5'-nucleotidase that catalyzes |
| GO:0008253 5'-nucleotidase activity | IDA PMID:1659319 Nucleoside phosphotransferase activity of human colon carcin... | ACCEPT | Summary: The enzyme isolated from human colon carcinoma acts preferentially on IMP and GMP as a 5'-nucleotidase. Direct evidence for the core catalytic function. Accept. Supporting Evidence: PMID:1659319 A cytosolic 5'-nucleotidase, acting preferentially on IMP and GMP, has been |
| GO:0050146 nucleoside phosphotransferase activity | IDA PMID:1659319 Nucleoside phosphotransferase activity of human colon carcin... | ACCEPT | Summary: Direct demonstration that the enzyme transfers the phosphate of nucleoside monophosphates to acceptor nucleosides (nucleoside phosphotransferase activity). Core catalytic activity; accept. Supporting Evidence: PMID:1659319 catalyzes also the transfer of the phosphate group of 5'-nucleoside monophosphates |
| GO:0005829 cytosol | IDA PMID:9371705 Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning a... | ACCEPT | Summary: Cytosolic localization of the enzyme, from the same study establishing the subcellular location. Core location; accept. (The part_of qualifier for a cellular-component annotation is atypical but the localization itself is correct.) Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0008253 5'-nucleotidase activity | IDA PMID:10092873 ATP and phosphate reciprocally affect subunit association of... | ACCEPT | Summary: Recombinant human High Km (IMP-specific) 5'-nucleotidase characterized biochemically, confirming 5'-nucleotidase activity and its regulation by ATP and phosphate. Core catalytic function; accept. Supporting Evidence: PMID:10092873 IMP-specific, High Km 5'-nucleotidase (EC 3.1.3.5) is an ubiquitous enzyme |
| GO:0042802 identical protein binding | IDA PMID:10092873 ATP and phosphate reciprocally affect subunit association of... | KEEP AS NON CORE | Summary: The native enzyme is oligomeric (~195 kDa native vs ~57 kDa subunit) and the C-terminal acidic tail governs subunit association, i.e. it self-associates. This supports identical protein binding (homo-oligomerization). Keep as non-core (structural self-association underlying the tetramer). Supporting Evidence: PMID:10092873 an important function of the polyglutamic acid tract in the process of association and dissociation of 5'-nucleotidase subunits |
| GO:0046037 GMP metabolic process | IDA PMID:1659319 Nucleoside phosphotransferase activity of human colon carcin... | ACCEPT | Summary: The enzyme acts preferentially on IMP and GMP, dephosphorylating GMP; direct evidence for participation in GMP metabolism. Core process; accept. Supporting Evidence: PMID:1659319 acting preferentially on IMP and GMP |
| GO:0046037 GMP metabolic process | IDA PMID:9371705 Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning a... | ACCEPT | Summary: The IMP/GMP-specific 5'-nucleotidase dephosphorylates GMP; direct evidence for a role in GMP metabolism. Core process; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Has the highest activities for IMP and GMP |
| GO:0046040 IMP metabolic process | IDA PMID:10092873 ATP and phosphate reciprocally affect subunit association of... | ACCEPT | Summary: The IMP-specific High Km 5'-nucleotidase dephosphorylates IMP; direct evidence for a role in IMP metabolism. Core process; accept. Supporting Evidence: PMID:10092873 IMP-specific, High Km 5'-nucleotidase (EC 3.1.3.5) is an ubiquitous enzyme |
| GO:0046040 IMP metabolic process | IDA PMID:1659319 Nucleoside phosphotransferase activity of human colon carcin... | ACCEPT | Summary: The enzyme acts preferentially on IMP; direct evidence for participation in IMP metabolism. Core process; accept. Supporting Evidence: PMID:1659319 acting preferentially on IMP and GMP |
| GO:0046040 IMP metabolic process | IDA PMID:9371705 Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning a... | ACCEPT | Summary: IMP/GMP-specific 5'-nucleotidase dephosphorylating IMP; direct evidence for IMP metabolism. Core process; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Has the highest activities for IMP |
| GO:0046054 dGMP metabolic process | IDA PMID:1659319 Nucleoside phosphotransferase activity of human colon carcin... | KEEP AS NON CORE | Summary: The enzyme also acts on the deoxy counterparts of IMP/GMP (5'-dGMP), supporting a role in dGMP metabolism. This is a lower-preference deoxynucleotide substrate; keep as non-core relative to the IMP/GMP core. Supporting Evidence: PMID:1659319 (mainly, 5'-IMP, 5'-GMP, and their deoxycounterparts) |
| GO:0046054 dGMP metabolic process | IDA PMID:9371705 Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning a... | KEEP AS NON CORE | Summary: cN-II dephosphorylates dGMP among its substrates; supports dGMP metabolism. Lower-preference deoxynucleotide substrate; keep as non-core. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt followed by dIMP, dGMP and XMP |
| GO:0005524 ATP binding | IDA PMID:21396942 Structural basis for the allosteric regulation and substrate... | ACCEPT | Summary: Structural study shows ATP binds cN-II at an allosteric effector site (residues 144/154/453/456) as an activator. ATP binding is genuine and functionally important (allosteric activation), though it is a regulatory rather than catalytic function. Accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Allosterically activated by various compounds including ATP |
| GO:0042802 identical protein binding | IDA PMID:21396942 Structural basis for the allosteric regulation and substrate... | KEEP AS NON CORE | Summary: Crystallographic study of the homotetrameric enzyme, in which effector binding glues subunits together, supporting self-association (identical protein binding). Keep as non-core (structural self-association underlying the tetramer). Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBUNIT: Homotetramer |
| GO:0008253 5'-nucleotidase activity | IDA PMID:21873433 Suppression of 5'-nucleotidase enzymes promotes AMP-activate... | ACCEPT | Summary: Direct 5'-nucleotidase activity attributed to NT5C2 in human myotubes (activity reduced on silencing). Core catalytic function; accept. Supporting Evidence: PMID:21873433 NT5C2 silencing decreased NT5 activity in the cytoplasmic fraction |
| GO:0000255 allantoin metabolic process | IDA PMID:21873433 Suppression of 5'-nucleotidase enzymes promotes AMP-activate... | KEEP AS NON CORE | Summary: Allantoin is a distal product of purine degradation; humans lack functional urate oxidase and do not normally produce allantoin enzymatically, so this MGI-curated term is peripheral to human cN-II function and not directly demonstrated for NT5C2 in the cited human-myotube study. Keep as non-core; it is at best an indirect, upstream contribution to purine catabolism. |
| GO:0005829 cytosol | IDA PMID:21873433 Suppression of 5'-nucleotidase enzymes promotes AMP-activate... | ACCEPT | Summary: Enzyme active in the cytoplasmic (cytosolic) fraction of human myotubes. Core location; accept. Supporting Evidence: PMID:21873433 NT5C2 silencing decreased NT5 activity in the cytoplasmic fraction |
| GO:0006204 IMP catabolic process | IDA PMID:21873433 Suppression of 5'-nucleotidase enzymes promotes AMP-activate... | ACCEPT | Summary: Direct evidence (from NT5C2 silencing altering nucleotide pools) for a role in IMP catabolism (IMP -> inosine + Pi). Core catabolic process; accept. Supporting Evidence: PMID:21873433 Using siRNA to silence NT5C2 expression in cultured human myotubes, we observed a 2-fold increase in the AMP/ATP ratio |
| GO:0005829 cytosol | TAS Reactome:R-HSA-2162066 | ACCEPT | Summary: Reactome traceable-author statement placing cN-II in the cytosol (in the context of carbovir/abacavir metabolism). Correct core location; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-74248 | ACCEPT | Summary: Reactome TAS cytosol annotation (in the (d)GMP/(d)IMP dephosphorylation reaction). Correct core location; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9754916 | ACCEPT | Summary: Reactome TAS cytosol annotation (NT5C2 tetramer phosphorylates ribavirin). Correct core location; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9755078 | ACCEPT | Summary: Reactome TAS cytosol annotation (NT5C2 tetramer dephosphorylates ribavirin-MP). Correct core location; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0008253 5'-nucleotidase activity | TAS PMID:7999131 Molecular cloning of human cytosolic purine 5'-nucleotidase. | ACCEPT | Summary: Traceable-author statement (original human cN-II cDNA cloning paper) for 5'-nucleotidase activity. Core catalytic function; accept. Supporting Evidence: file:human/NT5C2/NT5C2-uniprot.txt Broad specificity cytosolic 5'-nucleotidase that catalyzes |
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