ARL15 is a 204-residue Arf-like small GTPase, palmitoylated, that localizes to the Golgi and endolysosomes. It binds GTP. Its intrinsic GTPase activity is disputed: measurable hydrolysis has been reported, but structural work finds it weak, consistent with an alanine at the catalytic glutamine position. ARL15 binds the CBS-pair domains of the CNNM magnesium transporters (crystal structure with CNNM2), promotes their complex N-glycosylation, and inhibits CNNM2-mediated Mg2+ efflux and TRPM7-mediated divalent cation uptake. It also binds the MH2 domain of Smad4, relieving Smad4 autoinhibition so that Smad complexes assemble; Smad4 has been reported to act as its GTPase-activating protein, although this is contested. It regulates Golgi-to-surface cargo transport. Arl15 knockout mice have cleft palate, and ARL15 variants are associated with metabolic traits and adiponectin levels.
Definition: Any process that stops, prevents or reduces the frequency, rate or extent of the directed movement of magnesium ions across a membrane.
Justification: ARL15 (and PRL phosphatases) inhibit CNNM-mediated Mg2+ efflux by direct binding; GO has magnesium ion transmembrane transport (GO:1903830) but no regulation children. GO:0010960 magnesium ion homeostasis describes the outcome at the level of cellular Mg2+ content, not the regulation of transporter flux that ARL15 performs, so it is not a substitute.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003674 molecular_function | ND GO_REF:0000015 | REMOVE | Summary: Molecular_function (ND, no biological data available). Experimental data now exist: ARL15 binds GTP, hydrolyses it, binds CNNM magnesium transporters and Smad4, and regulates TGFbeta-family signalling. The no-data placeholder is superseded; removed. Reason: [PMID:37939768 "Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively."] [PMID:35834310 "Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome."] Supporting Evidence: PMID:37939768 Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. PMID:35834310 Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome. |
| GO:0003924 GTPase activity | IEA GO_REF:0000002 | ACCEPT | Summary: GTPase activity (IEA, InterPro). The evidence is contested. One study measured GTP hydrolysis by recombinant ARL15 (Km about 100 uM), and another reports Smad4 as its GTPase-activating protein. A structural study instead finds very weak GTP binding and low intrinsic GTPase activity. ARL15 has alanine in place of the catalytic glutamine, so those authors doubt that a GAP exists. Accepted, because measurable if weak hydrolysis has been reported and is not refuted, but the activity level and its regulation are disputed. Reason: [PMID:37939768 "Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively."] [PMID:37449820 "Our observation of very weak binding of GTP to ARL15 and low intrinsic GTPase activity conflicts with a recent report that ARL15 upregulates TGFβ family signaling by promoting the assembly of the Smad complex (Shi et al."] [PMID:37449820 "It is questionable whether ARL15 has catalytic activity, given the importance and prevalence of glutamine in related GTPases."] [PMID:37449820 "It is impossible to affirm that a GAP does not exist for ARL15, but this seems unlikely since, in presence of rapid exchange, ARL15 GTPase activity would constitute an unregulated, futile cycle depleting the cell of GTP."] Supporting Evidence: PMID:37939768 Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. PMID:37449820 Our observation of very weak binding of GTP to ARL15 and low intrinsic GTPase activity conflicts with a recent report that ARL15 upregulates TGFβ family signaling by promoting the assembly of the Smad complex (Shi et al. PMID:37449820 It is questionable whether ARL15 has catalytic activity, given the importance and prevalence of glutamine in related GTPases. |
| GO:0005515 protein binding | IPI PMID:16169070 A human protein-protein interaction network: a resource for ... | REMOVE | Summary: Protein binding (IPI) with PDE6D, from a proteome-scale yeast two-hybrid map. Generic protein binding carries no functional information and no more specific term is established for this interaction, so the row is removed. Removal does not mean the interaction is false. Reason: Removed under the generic protein-binding policy: GO:0005515 is uninformative on its own. |
| GO:0005515 protein binding | IPI PMID:16169070 A human protein-protein interaction network: a resource for ... | REMOVE | Summary: Protein binding (IPI) with UNC119, from a proteome-scale yeast two-hybrid map. Generic protein binding carries no functional information and no more specific term is established for this interaction, so the row is removed. Removal does not mean the interaction is false. Reason: Removed under the generic protein-binding policy: GO:0005515 is uninformative on its own. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: Protein binding (IPI) with PDE6D, from the HuRI binary yeast two-hybrid map. Generic protein binding carries no functional information and no more specific term is established for this interaction, so the row is removed. Removal does not mean the interaction is false. Reason: Removed under the generic protein-binding policy: GO:0005515 is uninformative on its own. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: Protein binding (IPI) with UNC119, from the HuRI binary yeast two-hybrid map. Generic protein binding carries no functional information and no more specific term is established for this interaction, so the row is removed. Removal does not mean the interaction is false. Reason: Removed under the generic protein-binding policy: GO:0005515 is uninformative on its own. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: Protein binding (IPI) with MEOX2, from the HuRI binary yeast two-hybrid map. Generic protein binding carries no functional information and no more specific term is established for this interaction, so the row is removed. Removal does not mean the interaction is false. Reason: Removed under the generic protein-binding policy: GO:0005515 is uninformative on its own. |
| GO:0005525 GTP binding | IEA GO_REF:0000002 | ACCEPT | Summary: GTP binding (IEA, InterPro). Purified ARL15 binds GTP and GDP, with GTP affinity about eight-fold lower, and the GTP-bound form binds its effectors; core function. Reason: [PMID:37449820 "Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg2+ efflux."] [PMID:37939768 "Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively."] Supporting Evidence: PMID:37449820 Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg2+ efflux. PMID:37939768 Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. |
| GO:0008150 biological_process | ND GO_REF:0000015 | REMOVE | Summary: Biological_process (ND, no biological data available). Experimental data now exist: ARL15 binds GTP, hydrolyses it, binds CNNM magnesium transporters and Smad4, and regulates TGFbeta-family signalling. The no-data placeholder is superseded; removed. Reason: [PMID:37939768 "Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively."] [PMID:35834310 "Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome."] Supporting Evidence: PMID:37939768 Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. PMID:35834310 Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome. |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | KEEP AS NON CORE | Summary: Extracellular exosome (HDA, PMID:19056867). A proteomic detection in exosome preparations. ARL15 is a membrane-anchored GTPase found at the plasma membrane and on endosomes, from which exosome cargo can derive, but it has no known exosomal function; kept as non-core. Reason: [PMID:37449820 "Both wild-type ARL15 and the R95A mutant localize to the plasma membrane as well as internal structures."] [PMID:35834310 "In addition to the Golgi, WT and AL-mutant Arl15-GFP were also detected at the plasma membrane (PM), early endosome (EE), late endosome (LE), and lysosome"] Supporting Evidence: PMID:37449820 Both wild-type ARL15 and the R95A mutant localize to the plasma membrane as well as internal structures. PMID:35834310 In addition to the Golgi, WT and AL-mutant Arl15-GFP were also detected at the plasma membrane (PM), early endosome (EE), late endosome (LE), and lysosome |
| GO:0070062 extracellular exosome | HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... | KEEP AS NON CORE | Summary: Extracellular exosome (HDA, PMID:23533145). A proteomic detection in exosome preparations. ARL15 is a membrane-anchored GTPase found at the plasma membrane and on endosomes, from which exosome cargo can derive, but it has no known exosomal function; kept as non-core. Reason: [PMID:37449820 "Both wild-type ARL15 and the R95A mutant localize to the plasma membrane as well as internal structures."] [PMID:35834310 "In addition to the Golgi, WT and AL-mutant Arl15-GFP were also detected at the plasma membrane (PM), early endosome (EE), late endosome (LE), and lysosome"] Supporting Evidence: PMID:37449820 Both wild-type ARL15 and the R95A mutant localize to the plasma membrane as well as internal structures. PMID:35834310 In addition to the Golgi, WT and AL-mutant Arl15-GFP were also detected at the plasma membrane (PM), early endosome (EE), late endosome (LE), and lysosome |
| GO:0036019 endolysosome | IDA PMID:35834310 Arl15 upregulates the TGFβ family signaling by promoting the... | NEW | Summary: Endolysosome (NEW, IDA). Besides the Golgi, tagged ARL15 is seen on early endosomes, late endosomes and lysosomes in HeLa cells. Its GTP-bound form co-localizes with the Smad4 MH2 domain there, the site of its Smad4-activating role. Reason: [PMID:35834310 "Arl15 localizes to the Golgi and endolysosome."] [PMID:35834310 "In addition to the Golgi, WT and AL-mutant Arl15-GFP were also detected at the plasma membrane (PM), early endosome (EE), late endosome (LE), and lysosome"] Supporting Evidence: PMID:35834310 Arl15 localizes to the Golgi and endolysosome. PMID:35834310 In addition to the Golgi, WT and AL-mutant Arl15-GFP were also detected at the plasma membrane (PM), early endosome (EE), late endosome (LE), and lysosome |
| GO:0141110 transporter inhibitor activity | IDA PMID:37449820 Structural insights into regulation of CNNM-TRPM7 divalent c... | NEW | Summary: Transporter inhibitor activity (NEW, IDA). ARL15 binds the CBS-pair domain of CNNM2 (crystal structure) and abolishes CNNM2-mediated Mg2+ efflux. Through CNNM binding it also suppresses TRPM7 divalent cation uptake, and the binding-deficient R95A mutant loses this effect. Reason: [PMID:37449820 "The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding."] [PMID:37449820 "Cells expressing both CNNM2 and ARL15 showed no efflux, thus demonstrating that, like PRL3, ARL15 inhibits CNNM protein activity."] [PMID:37449820 "ARL15 co-expression markedly decreased intracellular Zn2+ levels in TRPM7-expressing cells while expression of the ARL15 R95A mutant had no effect."] Supporting Evidence: PMID:37449820 The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding. PMID:37449820 Cells expressing both CNNM2 and ARL15 showed no efflux, thus demonstrating that, like PRL3, ARL15 inhibits CNNM protein activity. PMID:37449820 ARL15 co-expression markedly decreased intracellular Zn2+ levels in TRPM7-expressing cells while expression of the ARL15 R95A mutant had no effect. |
| GO:1904063 negative regulation of cation transmembrane transport | IDA PMID:37449820 Structural insights into regulation of CNNM-TRPM7 divalent c... | NEW | Summary: Negative regulation of cation transmembrane transport (NEW, IDA). ARL15 inhibits CNNM2 Mg2+ efflux and TRPM7 divalent cation influx by binding CNNMs, performing the inhibitory step itself. GO has no magnesium-specific regulation-of-transport term, so this parent is used and a magnesium-specific term is proposed in proposed_new_terms. Reason: [PMID:37449820 "Cells expressing both CNNM2 and ARL15 showed no efflux, thus demonstrating that, like PRL3, ARL15 inhibits CNNM protein activity."] [PMID:37449820 "ARL15 co-expression markedly decreased intracellular Zn2+ levels in TRPM7-expressing cells while expression of the ARL15 R95A mutant had no effect."] Supporting Evidence: PMID:37449820 Cells expressing both CNNM2 and ARL15 showed no efflux, thus demonstrating that, like PRL3, ARL15 inhibits CNNM protein activity. PMID:37449820 ARL15 co-expression markedly decreased intracellular Zn2+ levels in TRPM7-expressing cells while expression of the ARL15 R95A mutant had no effect. |
| GO:0005794 Golgi apparatus | IDA PMID:35834310 Arl15 upregulates the TGFβ family signaling by promoting the... | NEW | Summary: Golgi apparatus (NEW, IDA). Endogenous ARL15 co-localizes with golgin-245 in HeLa cells. In adipocytes palmitoylated ARL15 moves between Golgi compartments during differentiation, and Golgi localization depends on palmitoylation. Reason: [PMID:35834310 "Arl15 localizes to the Golgi and endolysosome."] [PMID:34779483 "ARL15 was predominantly co-localised with a marker of the cis face of Golgi at the preadipocyte stage and then translocated to other Golgi compartments after differentiation was induced."] [PMID:40241309 "Collectively, these studies implicate a functional role for Arl15 in regulating cargo transport from the Golgi to regulate cell surface processes."] Supporting Evidence: PMID:35834310 Arl15 localizes to the Golgi and endolysosome. PMID:34779483 ARL15 was predominantly co-localised with a marker of the cis face of Golgi at the preadipocyte stage and then translocated to other Golgi compartments after differentiation was induced. PMID:40241309 Collectively, these studies implicate a functional role for Arl15 in regulating cargo transport from the Golgi to regulate cell surface processes. |
| GO:0060391 positive regulation of SMAD protein signal transduction | IDA PMID:35834310 Arl15 upregulates the TGFβ family signaling by promoting the... | NEW | Summary: Positive regulation of SMAD protein signal transduction (NEW, IDA). GTP-bound ARL15 binds the Smad4 MH2 domain at endolysosomes and relieves Smad4 autoinhibition, enabling Smad-complex assembly; ARL15 positively regulates TGFbeta-family signalling. ARL15 performs the activating step itself. Reason: [PMID:35834310 "Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome."] [PMID:35834310 "The binding relieves the autoinhibition of Smad4, which is imposed by the intramolecular interaction between its MH1 and MH2 domains."] [PMID:35834310 "Our data further demonstrate that Arl15 positively regulates the TGFβ family signaling."] Supporting Evidence: PMID:35834310 Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome. PMID:35834310 The binding relieves the autoinhibition of Smad4, which is imposed by the intramolecular interaction between its MH1 and MH2 domains. PMID:35834310 Our data further demonstrate that Arl15 positively regulates the TGFβ family signaling. |
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Download this section (compressed HTML)Q: ARL15 was recovered with the lipid-binding chaperones PDE6D and UNC119 in independent two-hybrid screens. Since ARL15 is triply S-acylated, do these chaperones carry it between membranes?
Q: Do ARL15's CNNM and Smad4 roles act from the same compartment, and which explains the cleft palate of Arl15 knockout mice?
Experiment: Test whether the CNNM-binding-deficient R95A mutant still promotes Smad4 activation, to separate ARL15's two effector arms.
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