id: MODULE:ampk_energy_sensing title: AMPK energy sensing — LKB1-STRAD-MO25 or Ca2+/calmodulin-CAMKK2 Thr172 activation of the AMPK alpha/beta/gamma heterotrimer, PP2A/PPM1E/PPM1F/PP1-R6 inactivation, and TSC2-mTORC1, ACC and CPT1 outputs; PRKAA1/2, PRKAB1/2, PRKAG1/2/3, STK11, STRADA, CAB39, CALM1-3, CAMKK1/2, PPP2CA, PPM1E, PPM1F, PPP1CA/B, PPP1R3D, TSC1, TSC2 description: >- AMP-activated protein kinase (AMPK) is the principal cellular energy sensor of mammals. It is a heterotrimer of a catalytic alpha subunit (PRKAA1 or PRKAA2), a scaffolding beta subunit (PRKAB1 or PRKAB2) that carries a glycogen-binding domain and bridges alpha and gamma, and a regulatory gamma subunit (PRKAG1, PRKAG2 or PRKAG3) whose four tandem cystathionine-beta-synthase (CBS) repeats form the adenine nucleotide-binding sites. The kinase is active only when Thr172 in the alpha-subunit activation loop is phosphorylated. Two upstream kinases do this. The LKB1 complex, in which the kinase STK11 (LKB1) is held in an active conformation by the pseudokinase STRADA and the scaffold CAB39 (MO25alpha), is constitutively active, so its output is set by the AMPK side: when ATP production falls or consumption rises, AMP and ADP displace ATP from the gamma-subunit sites, which promotes Thr172 phosphorylation, protects the phosphate from phosphatases and (for AMP) allosterically activates the kinase. Alternatively, a rise in cytosolic calcium activates calmodulin, which activates the calmodulin-dependent protein kinase kinases, chiefly CAMKK2, and these phosphorylate Thr172 without any change in adenine nucleotides. The signal is terminated by dephosphorylation of Thr172 by protein phosphatase 2A, by the PPM-family phosphatases PPM1E and PPM1F, and, in pancreatic beta cells, by a protein phosphatase 1 holoenzyme targeted to AMPK by its regulatory subunit PPP1R3D (R6). Active AMPK switches off ATP-consuming processes and switches on ATP-producing ones. It phosphorylates TSC2, increasing the GTPase-activating activity of the TSC1-TSC2 complex towards RHEB, and it phosphorylates the mTORC1 subunit raptor; both inhibit mTORC1 and so protein synthesis and cell growth. It phosphorylates and inhibits acetyl-CoA carboxylase, lowering malonyl-CoA, which both reduces fatty acid synthesis and relieves malonyl-CoA inhibition of carnitine palmitoyltransferase 1, so that long-chain fatty acids enter mitochondria for beta-oxidation. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0000542 title: adenosine monophosphate-activated protein kinase (AMPK) signaling pathway statement: >- The module boundary follows the RGD Pathway Ontology term and its interactive diagram. The diagram draws AMPK alpha, beta and gamma as associated subunits, AMP, ADP and ATP associated with AMPK gamma, the Lkb1 complex, Camkk1 and Camkk2 (associated with calmodulin) positively affecting AMPK alpha, and Ppp2ca, Ppm1e, Ppm1f and "PP1 in AMPK" negatively affecting AMPK alpha. "AMPK targets" negatively affect the fatty acid biosynthetic, gluconeogenesis, glycogen biosynthetic and mTOR signalling pathways and positively affect fatty acid beta degradation and insulin-responsive glucose transport, all drawn as links to other pathway diagrams. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0000542.yaml). - source_id: GO:0061762 title: CAMKK-AMPK signaling cascade statement: >- The curated GO mapping for PW:0000542 in the project's PW-GO SSSOM file (skos:narrowMatch). It covers the calcium/CAMKK activation route only, so it is placed on that variant and not on the module as a whole. GO has no general AMPK signalling process term. - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: >- The RGD record text defines the heterotrimer, the two upstream kinase routes and the principal metabolic outputs used for the part order. supporting_text: AMPK is a heterotrimer composed of alpha-catalytic and beta and gamma-regulatory subunits. - source_id: PMID:21399626 title: Structure of mammalian AMPK and its regulation by ADP. statement: >- Primary structural paper stating the three effects of AMP binding to the gamma subunit (promoting Thr172 phosphorylation, protecting it from dephosphorylation, and allosteric activation) and showing that ADP also protects against dephosphorylation. supporting_text: AMPK is converted from an inactive form to a catalytically competent form by phosphorylation of the activation loop within the kinase domain notes: >- Derived from the RGD Pathway Ontology diagram PW:0000542 through the RGD_PATHWAY_ONTOLOGY project's diagram->module route. RGD curates 23 human genes to PW:0000542 (CAB39 CALM1 CALM2 CALM3 CAMKK1 CAMKK2 CPT1A PPM1E PPM1F PPP1CA PPP1CB PPP1R3D PPP2CA PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 STK11 STRADA TSC1). Twenty-two are modelled as participants. CPT1A is excluded as a participant and is covered by reference to the carnitine shuttle module. TSC2 is added although RGD does not list it, because the RGD record text states that AMPK acts on Tsc2 to inhibit mTOR signalling and TSC2 is the GAP subunit of the complex whose other subunit (TSC1) RGD does list. Boundary decisions. (1) Process term. The curated PW-GO mapping is a narrowMatch to GO:0061762 CAMKK-AMPK signaling cascade, which by definition starts with calcium-bound calmodulin binding CAMKK and ends with AMP-activated protein kinase activity. It does not cover the LKB1 route, the nucleotide-sensing step or the outputs, so it is used only on the CAMKK variant. The module concept is cellular response to glucose starvation GO:0042149, which PRKAA1 and PRKAA2 carry by IDA and IBA and which the human glucose-starvation GO-CAMs (gomodel:698e557b00001137, gomodel:6482692800001813, gomodel:6482692800001739) use as the parent process of AMPK activity. Energy homeostasis GO:0097009 (ISS/TAS on PRKAA1) is broader and is mentioned here only. Calcium-triggered AMPK activation is not a glucose-starvation response; the module concept describes the energy-stress core, and the CAMKK variant carries its own process term. (2) The heterotrimer is one PROTEIN_COMPLEX annoton (GO:0031588 nucleotide-activated protein kinase complex) with three active units, one per subunit class, each a FAMILY with the human paralogues as representative members. Any alpha can combine with any beta and any gamma (2 x 2 x 3 = 12 combinations, more with splice forms); this is recorded on the family descriptors rather than as variant sets, because the paralogues share the same molecular function and differ in tissue distribution and subcellular targeting rather than in the step they perform. Molecular functions follow the experimental GO annotations: AMP-activated protein kinase activity GO:0004679 for the alpha subunits (IDA for PRKAA1 and PRKAA2) and protein kinase regulator activity GO:0019887 for the gamma subunits (IDA for PRKAG1, PRKAG2 and PRKAG3). The beta subunits have no experimental molecular function other than binding, so their unit carries none; PRKAB2 carries GO:0004679 by IDA, which is the activity of the complex, not of the non-catalytic beta subunit (noted below as a possible upstream issue). (3) Upstream kinases are a variant set on the axis of the activating signal (energy stress with constitutive LKB1, or a calcium rise through CAMKK), selection ONE_OR_MORE because many cells use both. The LKB1 complex is modelled with GO:1902554 serine/threonine protein kinase complex (GO has no LKB1-specific complex term) with STK11 protein serine/threonine kinase activity GO:0004674 (IDA) and STRADA and CAB39 protein serine/threonine kinase activator activity GO:0043539 (IDA for both). STRADA is a pseudokinase; its GO:0004672 protein kinase activity IDA (from PMID:12805220, which reports phosphorylation of STRAD by LKB1 in the complex) is noted below as a possible upstream error. The CAMKK route uses calmodulin (CALM1, CALM2 and CALM3 encode an identical protein, so one FAMILY annoton with three representative members) with GO:0043539, the CALM1 gene-review core function, and CAMKK1/CAMKK2 with calcium/calmodulin-dependent protein kinase activity GO:0004683, the activity named in the GO:0061762 definition. GO:0004683 is IBA/IEA only for CAMKK1 and IEA only for CAMKK2: neither has an experimental MF row for it, although the cited papers show in vitro phosphorylation and activation of AMPK by CAMKKbeta. CAMKK2 is the main AMPK kinase of the pair (PMID:16054095); CAMKK1 is modelled because RGD draws it and both isoforms act as AMPK kinases in cells (PMID:15980064). (4) Inactivation is a variant set of Thr172 phosphatases with selection ONE_OR_MORE: PP2A (PPP2CA, GO:0004722 IDA/EXP), the PPM pair PPM1E and PPM1F (GO:0004722 IDA), and PP1-R6 (PPP1CA/PPP1CB with PPP1R3D). The PP1-R6 holoenzyme is modelled with GO:0000164 protein phosphatase type 1 complex, whose definition (catalytic subunit plus a regulatory subunit that dictates substrate specificity) fits the R6-targeted enzyme. PPP1R3D has no experimental molecular function (protein phosphatase 1 binding GO:0008157 is IBA only), so its unit carries a role statement only. The PP2A step is drawn on the catalytic subunit alone; the B56delta regulatory subunit (PPP2R5D) implicated in PMID:24412756 is not on the RGD list and is not modelled. Phosphatase activity on AMPK is regulatory to this module; the phosphatase annotons carry protein dephosphorylation GO:0006470, not the module process term. (5) Outputs. Under the substrate-vs-participant rule, AMPK substrates whose phosphorylation is the output (raptor, ACC1/ACC2, TBC1D1, HMG-CoA reductase and others) are not participants. The TSC1-TSC2 complex is modelled as a part because it does work in the module: its GTPase activator activity GO:0005096 (IDA for TSC2) on RHEB is the step by which AMPK phosphorylation is relayed to mTORC1, and RGD names it. TSC1 is included as a unit of the TSC1-TSC2 complex GO:0033596 with protein folding chaperone GO:0044183 (IDA), the role it has in the TSC1 GO-CAM gomodel:65a1f4f800000922, where it stabilises TSC2; it is not itself phosphorylated by AMPK in the cited work. The downstream mTORC1 step is an optional part by module_ref to pi3k_akt_mtor#mtorc1_activation, so mTORC1 and RHEB are not re-modelled here; direct raptor phosphorylation by AMPK (PMID:18439900) is a second connection to that part. The lipid outputs are optional parts by module_ref to fatty_acid_de_novo_synthesis#malonyl_coa_synthesis (ACC, inhibited by AMPK phosphorylation) and carnitine_shuttle#cpt1_step (CPT1, inhibited by malonyl-CoA); CPT1A is the RGD gene for the latter and is not re-modelled. The other RGD outputs (gluconeogenesis, glycogen synthesis, insulin-responsive glucose transport via TBC1D1, fatty acid beta-oxidation) are drawn by RGD as links to other PW diagrams (PW:0000641, PW:0000532, PW:0000639, PW:0000738, PW:0000029, PW:0000180) and are not modelled; those PW ids are mentioned here only and are not evidence source_ids. Metformin action (complex I inhibition raising AMP) is upstream context, not a module part. (6) Location. The module context is cytosol. AMPK also acts in the nucleus and at the lysosomal surface (the AXIN1-LKB1 route of gomodel:698e557b00001137 puts STK11 on late endosomes), which is described in prose only. TSC2 is located on the lysosomal membrane, as in the GO-CAMs. Comparator check for GO:0042149. Only the AMPK catalytic subunits are given this process on their own annotons; the LKB1 complex, calmodulin, the CAMKKs, the phosphatases and TSC1/TSC2 carry their own functions and are not asserted to be involved in it (STK11 has GO:0042149 by ISS only). Possible upstream errors noticed: STRADA (Q7RTN6) carries GO:0004672 protein kinase activity by IDA (PMID:12805220) although that paper describes STRAD as a pseudokinase lacking residues indispensable for catalytic activity; PRKAB2 (O43741) carries GO:0004679 AMP-activated protein kinase activity by IDA on a non-catalytic subunit (contributes_to would fit better); CAMKK2 (Q96RR4) carries GO:0004713 protein tyrosine kinase activity by TAS; in gomodel:698e557b00001137 STK11 is typed as protein serine kinase activity GO:0106310, although the AMPK site it phosphorylates is Thr172 (GO:0004674 would fit). GO-CAM coverage is linked under gocam_associations. No GO-CAM in gocams/index.tsv covers PRKAB1/2, PRKAG1-3, STRADA, CAB39, CAMKK1/2, PPM1E/F, PPP1R3D or PP1/PP2A acting on AMPK. Gene reviews exist for CALM1, CALM2, CALM3, PPP2CA and CPT1A; the other members have no review yet. The fly counterparts are modules/dmel_ampk_complex.yaml and modules/dmel_lkb1_strad_mo25_complex.yaml (concrete Drosophila modules, not module_ref'd). PANTHER family ids and PTNs are deliberately not asserted. module: id: ampk_energy_sensing label: AMPK energy sensing and signalling module_type: SIGNALING_PATHWAY concepts: - preferred_term: cellular response to glucose starvation term: id: GO:0042149 label: cellular response to glucose starvation description: >- Energy-stress response carried by AMPK activity in the human glucose-starvation GO-CAMs. GO has no general AMPK signalling term; the curated PW mapping GO:0061762 is placed on the CAMKK variant. context: taxa: - preferred_term: Homo sapiens term: id: NCBITaxon:9606 label: Homo sapiens cellular_components: - preferred_term: cytosol term: id: GO:0005829 label: cytosol parts: - order: 1 role: Thr172 phosphorylation of the AMPK alpha subunit by an upstream kinase node: id: ampk_upstream_kinases label: Upstream AMPK kinases (LKB1 complex or Ca2+/calmodulin-CAMKK) module_type: REGULATORY_STEP description: >- AMPK is active only when Thr172 in the alpha-subunit activation loop is phosphorylated. The constitutively active LKB1 complex supplies this phosphorylation under energy stress, when nucleotide binding to AMPK gamma makes the site available; calcium-activated CAMKKs supply it independently of adenine nucleotide levels. variant_sets: - id: ampk_kinase_route label: AMPK kinase route axis: activating signal (energy stress via constitutive LKB1, or a cytosolic Ca2+ rise via calmodulin-CAMKK) selection: ONE_OR_MORE notes: >- Many cell types use both routes; LKB1-deficient cells retain calcium-stimulated AMPK phosphorylation through CAMKKbeta. evidence: - source_id: PMID:16054096 statement: AMPK is phosphorylated and activated on Thr172 by at least two upstream kinases, LKB1 and CAMKKbeta. supporting_text: These results demonstrate that AMPK is regulated by at least two upstream kinases and suggest that AMPK may play a role in Ca(2+)-mediated signal transduction pathways. - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: RGD text names the LKB1 complex as the constitutive upstream kinase and CAMKK as the calcium-activated alternative. supporting_text: In certain cell types, Thr172 can be phosphorylated by calmodulin-dependent protein kinase kinases (CAmKK), in turn activated by calcium/calmodulin. variants: - id: lkb1_route label: LKB1-STRADA-CAB39 complex (energy-stress route) module_type: PROTEIN_COMPLEX description: >- STK11 (LKB1) is held in an active conformation by the pseudokinase STRADA, which binds it as a pseudosubstrate, and by the scaffold CAB39 (MO25alpha), which binds STRADA and the LKB1 activation loop. The complex is constitutively active and is anchored in the cytoplasm. annotons: - id: lkb1_complex_kinase label: LKB1-STRAD-MO25 kinase complex participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: LKB1-STRAD-MO25 complex term: id: GO:1902554 label: serine/threonine protein kinase complex active_units: - id: stk11_unit label: LKB1 catalytic subunit participant: selector_type: GENE_PRODUCT gene_product: preferred_term: STK11 (LKB1) term: id: UniProtKB:Q15831 label: Serine/threonine-protein kinase STK11 role: Catalytic subunit that phosphorylates AMPK alpha Thr172. function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity - id: strada_unit label: STRADalpha pseudokinase activator participant: selector_type: GENE_PRODUCT gene_product: preferred_term: STRADA term: id: UniProtKB:Q7RTN6 label: STE20-related kinase adapter protein alpha role: Pseudokinase that binds LKB1 as a pseudosubstrate and promotes its active conformation and cytoplasmic localisation. function: preferred_term: protein serine/threonine kinase activator activity term: id: GO:0043539 label: protein serine/threonine kinase activator activity - id: cab39_unit label: MO25alpha scaffold participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CAB39 (MO25alpha) term: id: UniProtKB:Q9Y376 label: Calcium-binding protein 39 role: Scaffold that stabilises the LKB1-STRADA complex and the LKB1 activation loop. function: preferred_term: protein serine/threonine kinase activator activity term: id: GO:0043539 label: protein serine/threonine kinase activator activity function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity substrates: - preferred_term: Thr172 in the activation loop of AMPK alpha (PRKAA1, PRKAA2) locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Constitutive AMPK kinase. STK11 GO:0004674 is IDA; STRADA and CAB39 GO:0043539 are IDA. LKB1 also activates the twelve AMPK-related kinases, which are outside this module. evidence: - source_id: PMID:14976552 statement: LKB1 in complex with STRAD and MO25 phosphorylates and activates AMPK; LKB1 catalytic activity and both partners are needed. supporting_text: We recently demonstrated that the LKB1 tumour suppressor kinase, in complex with the pseudokinase STRAD and the scaffolding protein MO25, phosphorylates and activates AMP-activated protein kinase (AMPK). - source_id: PMID:19892943 statement: STRADalpha binds LKB1 as a pseudosubstrate and, with MO25alpha, promotes the active LKB1 conformation. supporting_text: STRADalpha adopts a closed conformation typical of active protein kinases and binds LKB1 as a pseudosubstrate. STRADalpha and MO25alpha promote the active conformation of LKB1, which is stabilized by MO25alpha interacting with the LKB1 activation loop. - source_id: PMID:12805220 statement: STRAD is a catalytically deficient STE20-like pseudokinase that activates LKB1. supporting_text: STRAD consists of a STE20- like kinase domain, but lacks several residues that are indispensable for intrinsic catalytic activity. - source_id: PMID:14517248 statement: MO25alpha binds the C-terminus of STRADalpha, anchors LKB1 in the cytoplasm and stimulates LKB1 activity about tenfold. supporting_text: Moreover, MO25alpha enhances the formation of the LKB1-STRADalpha complex in vivo, stimulating the catalytic activity of LKB1 approximately 10-fold. - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: RGD describes the Lkb1 complex as one catalytic and two regulatory subunits and as constitutively active. supporting_text: The upstream kinase, known as Lkb1, is a complex of one catalytic and two regulatory subunits; Lkb1 is believed to be 'constitutively active'. gocam_associations: - model: gomodel:698e557b00001137 activity: gomodel:698e557b00001137/698e557b00001307 title: Inhibition of mTORC1 signaling by the AXIN1-STK11 axis in response to glucose starvation (Human). description: >- STK11 activity (typed GO:0106310 protein serine kinase activity) directly positively regulating PRKAA1 AMP-activated protein kinase activity; STK11 is modelled alone, without STRADA or CAB39. - model: gomodel:698e557b00001137 activity: gomodel:698e557b00001137/698e557b00001342 title: Inhibition of mTORC1 signaling by the AXIN1-STK11 axis in response to glucose starvation (Human). description: The matching STK11 activity directly positively regulating PRKAA2. - id: camkk_route label: Ca2+/calmodulin-CAMKK route module_type: SIGNALING_PATHWAY description: >- A rise in cytosolic calcium loads calmodulin, which binds and activates the calmodulin-dependent protein kinase kinases. CAMKK2 (CaMKKbeta) phosphorylates AMPK Thr172 much faster than CAMKK1 and is required for calcium-stimulated AMPK activation in LKB1-deficient cells; this route operates without a change in adenine nucleotides. concepts: - preferred_term: CAMKK-AMPK signaling cascade term: id: GO:0061762 label: CAMKK-AMPK signaling cascade description: The curated narrowMatch for PW:0000542, specific to this route. annotons: - id: calmodulin_camkk_activator label: Calcium-bound calmodulin participant: selector_type: FAMILY family: preferred_term: calmodulin (CALM1, CALM2, CALM3) description: >- Three human genes encode an identical calmodulin protein; any of them can fill this role. representative_members: - preferred_term: CALM1 term: id: UniProtKB:P0DP23 label: Calmodulin-1 - preferred_term: CALM2 term: id: UniProtKB:P0DP24 label: Calmodulin-2 - preferred_term: CALM3 term: id: UniProtKB:P0DP25 label: Calmodulin-3 function: preferred_term: protein serine/threonine kinase activator activity term: id: GO:0043539 label: protein serine/threonine kinase activator activity processes: - preferred_term: CAMKK-AMPK signaling cascade term: id: GO:0061762 label: CAMKK-AMPK signaling cascade locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Calcium sensor that binds and activates CAMKK; GO:0043539 is IDA on CALM1 and is the CALM1 gene-review core function. The GO:0061762 definition begins with calmodulin binding calcium and then CAMKK. evidence: - source_id: PMID:16054095 statement: Calcium ionophores stimulate AMPK in LKB1-deficient cells through CaMKKbeta. supporting_text: We now report that there is a significant basal activity and phosphorylation of AMPK in LKB1-deficient cells that can be stimulated by Ca2+ ionophores, and studies using the CaMKK inhibitor STO-609 and isoform-specific siRNAs show that CaMKKbeta is required for this effect. - id: camkk2_ampk_kinase label: CAMKK2 (CaMKKbeta) AMPK kinase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CAMKK2 term: id: UniProtKB:Q96RR4 label: Calcium/calmodulin-dependent protein kinase kinase 2 function: preferred_term: calcium/calmodulin-dependent protein kinase activity term: id: GO:0004683 label: calcium/calmodulin-dependent protein kinase activity substrates: - preferred_term: Thr172 in the activation loop of AMPK alpha (PRKAA1, PRKAA2) processes: - preferred_term: CAMKK-AMPK signaling cascade term: id: GO:0061762 label: CAMKK-AMPK signaling cascade locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Principal calcium-activated AMPK kinase. GO:0004683 is IEA only for CAMKK2 (no experimental MF row), although the cited work shows that CaMKKbeta phosphorylates and activates AMPK in vitro; GO:0061762 is IMP/IBA. evidence: - source_id: PMID:16054096 statement: CaMKKbeta phosphorylates and activates AMPK in vitro, and its knockdown nearly abolishes AMPK activation. supporting_text: CaMKKbeta isolated from rat brain or expressed in E. coli phosphorylates and activates AMPK in vitro. - source_id: PMID:16054095 statement: CaMKKbeta activates AMPK much faster than CaMKKalpha. supporting_text: CaMKKbeta also activates AMPK much more rapidly than CaMKKalpha in cell-free assays. - id: camkk1_ampk_kinase label: CAMKK1 (CaMKKalpha) AMPK kinase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CAMKK1 term: id: UniProtKB:Q8N5S9 label: Calcium/calmodulin-dependent protein kinase kinase 1 function: preferred_term: calcium/calmodulin-dependent protein kinase activity term: id: GO:0004683 label: calcium/calmodulin-dependent protein kinase activity substrates: - preferred_term: Thr172 in the activation loop of AMPK alpha locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Minor calcium-activated AMPK kinase drawn by RGD. GO:0004683 is IBA/IEA only. Not asserted to be in GO:0061762, which CAMKK1 does not carry in GOA. evidence: - source_id: PMID:15980064 statement: siRNA against either CaMKKalpha or CaMKKbeta reduces ionomycin- and 2-deoxyglucose-stimulated AMPK Thr172 phosphorylation in LKB1-deficient HeLa cells. supporting_text: These data indicate that the CaMKKs function in intact cells as AMPKKs, predicting wider roles for these kinases in regulating AMPK activity in vivo. connections: - source: calmodulin_camkk_activator target: camkk2_ampk_kinase connection_type: POSITIVELY_REGULATES description: Ca2+-calmodulin binds and activates CAMKK2. - source: calmodulin_camkk_activator target: camkk1_ampk_kinase connection_type: POSITIVELY_REGULATES description: Ca2+-calmodulin binds and activates CAMKK1. - order: 2 role: adenine-nucleotide sensing and AMPK kinase activity node: id: ampk_heterotrimer label: AMPK alpha/beta/gamma heterotrimer senses AMP/ADP and phosphorylates its targets module_type: PROTEIN_COMPLEX description: >- The gamma subunit's CBS repeats bind AMP, ADP or ATP competitively. AMP or ADP binding promotes Thr172 phosphorylation and protects it from dephosphorylation, and AMP binding also allosterically activates the kinase; ATP antagonises these effects. The beta subunit bridges alpha and gamma and carries a glycogen-binding domain. The phosphorylated alpha subunit phosphorylates metabolic and growth-control substrates. annotons: - id: ampk_complex_kinase label: AMPK heterotrimer participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: AMP-activated protein kinase complex term: id: GO:0031588 label: nucleotide-activated protein kinase complex active_units: - id: ampk_alpha_unit label: AMPK alpha catalytic subunit participant: selector_type: FAMILY family: preferred_term: AMPK catalytic alpha subunits description: >- Two human paralogues; either can pair with any beta and gamma subunit. representative_members: - preferred_term: PRKAA1 term: id: UniProtKB:Q13131 label: 5'-AMP-activated protein kinase catalytic subunit alpha-1 - preferred_term: PRKAA2 term: id: UniProtKB:P54646 label: 5'-AMP-activated protein kinase catalytic subunit alpha-2 role: Catalytic subunit; its Thr172 is the site of activating phosphorylation. function: preferred_term: AMP-activated protein kinase activity term: id: GO:0004679 label: AMP-activated protein kinase activity - id: ampk_beta_unit label: AMPK beta scaffolding subunit participant: selector_type: FAMILY family: preferred_term: AMPK beta subunits description: >- Two human paralogues with an N-terminal glycogen-binding (carbohydrate-binding module) domain and a C-terminal domain that binds alpha and gamma. representative_members: - preferred_term: PRKAB1 term: id: UniProtKB:Q9Y478 label: 5'-AMP-activated protein kinase subunit beta-1 - preferred_term: PRKAB2 term: id: UniProtKB:O43741 label: 5'-AMP-activated protein kinase subunit beta-2 role: >- Scaffold that bridges the alpha and gamma subunits and binds glycogen; no experimental GO molecular function other than binding is recorded (the PRKAB2 GO:0004679 IDA row describes the complex's activity). - id: ampk_gamma_unit label: AMPK gamma nucleotide-sensing subunit participant: selector_type: FAMILY family: preferred_term: AMPK gamma subunits description: >- Three human paralogues, each with four tandem CBS repeats forming the AMP/ADP/ATP sites. PRKAG2 CBS-domain mutations cause Wolff-Parkinson-White syndrome. representative_members: - preferred_term: PRKAG1 term: id: UniProtKB:P54619 label: 5'-AMP-activated protein kinase subunit gamma-1 - preferred_term: PRKAG2 term: id: UniProtKB:Q9UGJ0 label: 5'-AMP-activated protein kinase subunit gamma-2 - preferred_term: PRKAG3 term: id: UniProtKB:Q9UGI9 label: 5'-AMP-activated protein kinase subunit gamma-3 role: Binds AMP, ADP or ATP competitively and transmits the cellular energy state to the alpha subunit. function: preferred_term: protein kinase regulator activity term: id: GO:0019887 label: protein kinase regulator activity function: preferred_term: AMP-activated protein kinase activity term: id: GO:0004679 label: AMP-activated protein kinase activity targets: - preferred_term: TSC2 - preferred_term: raptor (RPTOR) - preferred_term: acetyl-CoA carboxylase (ACACA, ACACB) - preferred_term: TBC1D1 processes: - preferred_term: cellular response to glucose starvation term: id: GO:0042149 label: cellular response to glucose starvation locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- The energy sensor and effector kinase of the module. GO:0004679 is IDA for PRKAA1 and PRKAA2, GO:0019887 is IDA for PRKAG1, PRKAG2 and PRKAG3, and GO:0042149 is IDA/IBA for both alpha subunits. evidence: - source_id: PMID:21399626 statement: AMP binding to the gamma domain promotes Thr172 phosphorylation, protects against dephosphorylation and allosterically activates; ADP binding protects without allosteric activation. supporting_text: Here we show that ADP binding to just one of the two exchangeable AXP (AMP/ADP/ATP) binding sites on the regulatory domain protects the enzyme from dephosphorylation, although it does not lead to allosteric activation. - source_id: PMID:14722619 statement: Tandem CBS-domain pairs of the AMPK gamma subunit bind AMP and ATP, and disease mutations impair this binding. supporting_text: This shows that tandem pairs of CBS domains act, in most cases, as sensors of cellular energy status and, as such, represent a newly identified class of binding domain for adenosine derivatives. - source_id: PMID:15980064 statement: AMPK activity depends absolutely on phosphorylation of alpha Thr172 by an AMPK kinase. supporting_text: AMPK activity is absolutely dependent upon phosphorylation of AMPKalphaThr-172 in its activation loop by one or more AMPK kinases (AMPKKs). - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: RGD describes competitive AMP/ADP/ATP binding to the gamma-subunit CBS repeats. supporting_text: ATP antagonizes the effect of AMP; both AMP and ATP bind in a mutually exclusive manner to the Bateman ( CBS ) domains of the gamma subunit. gocam_associations: - model: gomodel:698e557b00001137 activity: gomodel:698e557b00001137/698e557b00001319 title: Inhibition of mTORC1 signaling by the AXIN1-STK11 axis in response to glucose starvation (Human). description: PRKAA1 AMP-activated protein kinase activity (GO:0004679), directly positively regulated by STK11, part of GO:0042149. - model: gomodel:698e557b00001137 activity: gomodel:698e557b00001137/698e557b00001353 title: Inhibition of mTORC1 signaling by the AXIN1-STK11 axis in response to glucose starvation (Human). description: PRKAA2 AMP-activated protein kinase activity (GO:0004679), directly positively regulated by STK11. - model: gomodel:6482692800001813 activity: gomodel:6482692800001813/6482692800001918 title: Inhibition of the canonical mTORC1 signaling following phosphorylation of TSC2 by AMPK in response to glucose starvation (Human) description: PRKAA1 GO:0004679 acting on TSC2. - model: gomodel:6482692800001813 activity: gomodel:6482692800001813/6482692800001928 title: Inhibition of the canonical mTORC1 signaling following phosphorylation of TSC2 by AMPK in response to glucose starvation (Human) description: PRKAA2 GO:0004679 acting on TSC2. - model: gomodel:6482692800001739 activity: gomodel:6482692800001739/6482692800001783 title: Inhibition of the canonical mTORC1 signaling via phosphorylation of RPTOR by AMPK in response to glucose starvation (Human) description: PRKAA1 GO:0004679 acting on raptor. - model: gomodel:6482692800001739 activity: gomodel:6482692800001739/6482692800001792 title: Inhibition of the canonical mTORC1 signaling via phosphorylation of RPTOR by AMPK in response to glucose starvation (Human) description: PRKAA2 GO:0004679 acting on raptor. - order: 3 role: termination by Thr172 dephosphorylation node: id: ampk_thr172_dephosphorylation label: Thr172 phosphatases inactivate AMPK module_type: REGULATORY_STEP description: >- When ATP is restored, ATP displaces AMP/ADP from the gamma subunit, Thr172 becomes accessible to protein phosphatases, and AMPK is switched off. Three phosphatase classes are implicated; which dominates depends on cell type. variant_sets: - id: ampk_thr172_phosphatase label: AMPK Thr172 phosphatase axis: phosphatase family (PPP-family PP2A, PPM-family PPM1E/PPM1F, or R6-targeted PP1) selection: ONE_OR_MORE notes: >- RGD draws all three as negatively affecting AMPK alpha. The PPM and PP1-R6 evidence comes from depletion experiments in cells; none of the three has been shown to be the sole Thr172 phosphatase. evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: RGD text attributes protection of phospho-Thr172 from dephosphorylation to nucleotide binding at gamma-subunit site 3. supporting_text: Binding of AMP to site 1 is believed to confer allosteric activation while binding of AMP or ADP to site 3 is thought to protect threonine 172 from dephosphorylation. variants: - id: pp2a_dephosphorylation label: PP2A module_type: REGULATORY_STEP annotons: - id: ppp2ca_ampk_phosphatase label: PP2A catalytic subunit alpha participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PPP2CA term: id: UniProtKB:P67775 label: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform function: preferred_term: protein serine/threonine phosphatase activity term: id: GO:0004722 label: protein serine/threonine phosphatase activity substrates: - preferred_term: phospho-Thr172 of AMPK alpha processes: - preferred_term: protein dephosphorylation term: id: GO:0006470 label: protein dephosphorylation locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- PP2A catalytic subunit; GO:0004722 is IDA/EXP in GOA and is the PPP2CA gene-review core function. The B56delta regulatory subunit implicated in the cited work is not modelled. evidence: - source_id: PMID:24412756 statement: PP2A dephosphorylates AMPK alpha at Thr172 in metal-treated cells. supporting_text: Here, we demonstrate that protein phosphatase 2A (PP2A) regulates expression of HSP70 and HSP27 via dephosphorylation of an AMP-activated protein kinase α subunit (AMPKα) at Thr172. - id: ppm1e_ppm1f_dephosphorylation label: PPM1E and PPM1F module_type: REGULATORY_STEP annotons: - id: ppm1e_ampk_phosphatase label: PPM1E participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PPM1E term: id: UniProtKB:Q8WY54 label: Protein phosphatase 1E function: preferred_term: protein serine/threonine phosphatase activity term: id: GO:0004722 label: protein serine/threonine phosphatase activity substrates: - preferred_term: phospho-Thr172 of AMPK alpha processes: - preferred_term: protein dephosphorylation term: id: GO:0006470 label: protein dephosphorylation role_description: >- Mg2+/Mn2+-dependent PPM phosphatase; depletion raises AMPK Thr172 phosphorylation about threefold. GO:0004722 is IDA in GOA. evidence: - source_id: PMID:20801214 statement: Depletion of PPM1E increases AMPK alpha Thr172 phosphorylation in HEK293 cells. supporting_text: Depletion of Ppm1E, but not Ppm1A, using lentiviral-mediated stable gene silencing, increased AMPKα-Thr172 phosphorylation approximately three fold in HEK293 cells. - id: ppm1f_ampk_phosphatase label: PPM1F participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PPM1F term: id: UniProtKB:P49593 label: Protein phosphatase 1F function: preferred_term: protein serine/threonine phosphatase activity term: id: GO:0004722 label: protein serine/threonine phosphatase activity substrates: - preferred_term: phospho-Thr172 of AMPK alpha processes: - preferred_term: protein dephosphorylation term: id: GO:0006470 label: protein dephosphorylation role_description: >- PPM1E paralogue; the evidence that it dephosphorylates AMPK is weaker ("probably") than for PPM1E. GO:0004722 is IDA/IMP in GOA. evidence: - source_id: PMID:20801214 statement: PPM1E and probably PPM1F are AMPK phosphatases in cells. supporting_text: The data indicate that Ppm1E and probably PpM1F are in cellulo AMPK phosphatases and that Ppm1E is a potential anti-diabetic drug target. - id: pp1_r6_dephosphorylation label: PP1-R6 (PPP1CA/PPP1CB with PPP1R3D) module_type: PROTEIN_COMPLEX description: >- The PP1 regulatory subunit R6 binds the AMPK beta subunit and recruits the PP1 catalytic subunit to dephosphorylate alpha Thr172 when glucose is high, shown in pancreatic beta cells. annotons: - id: pp1_r6_ampk_phosphatase label: PP1-R6 holoenzyme participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: PP1-R6 holoenzyme term: id: GO:0000164 label: protein phosphatase type 1 complex active_units: - id: pp1_catalytic_unit label: PP1 catalytic subunit participant: selector_type: FAMILY family: preferred_term: PP1 catalytic subunits (PPP1CA, PPP1CB) description: The two PP1 catalytic isoforms on the RGD list; the cited study does not resolve the isoform. representative_members: - preferred_term: PPP1CA term: id: UniProtKB:P62136 label: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit - preferred_term: PPP1CB term: id: UniProtKB:P62140 label: Serine/threonine-protein phosphatase PP1-beta catalytic subunit role: Catalytic subunit that removes the Thr172 phosphate. function: preferred_term: protein serine/threonine phosphatase activity term: id: GO:0004722 label: protein serine/threonine phosphatase activity - id: ppp1r3d_unit label: R6 targeting subunit participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PPP1R3D (R6) term: id: UniProtKB:O95685 label: Protein phosphatase 1 regulatory subunit 3D role: >- Binds the AMPK beta subunit and recruits PP1; no experimental GO molecular function is recorded (GO:0008157 protein phosphatase 1 binding is IBA only). function: preferred_term: protein serine/threonine phosphatase activity term: id: GO:0004722 label: protein serine/threonine phosphatase activity substrates: - preferred_term: phospho-Thr172 of AMPK alpha processes: - preferred_term: protein dephosphorylation term: id: GO:0006470 label: protein dephosphorylation locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Glucose-induced AMPK inactivation in beta cells. GO:0004722 is IDA for PPP1CA and TAS/IBA for PPP1CB. evidence: - source_id: PMID:20724523 statement: R6 binds AMPK beta and recruits PP1 to dephosphorylate alpha Thr172 in MIN6 beta cells. supporting_text: R6 interacts physically with the β-subunit of the AMPK complex and recruits PP1 to dephosphorylate the catalytic α-subunit on Thr172. - order: 4 role: relay to mTORC1 through AMPK-phosphorylated TSC2 node: id: ampk_tsc_relay label: AMPK-activated TSC1-TSC2 complex inactivates RHEB module_type: PROTEIN_COMPLEX description: >- Under energy stress AMPK phosphorylates TSC2 and enhances the GTPase-activating activity of the TSC1-TSC2 complex towards RHEB, so less RHEB-GTP is available to activate mTORC1 on the lysosome. This is the opposite of AKT phosphorylation of TSC2 downstream of insulin, which inactivates the complex. annotons: - id: tsc_complex_gap label: TSC1-TSC2 GAP complex participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: TSC1-TSC2 complex term: id: GO:0033596 label: TSC1-TSC2 complex active_units: - id: tsc2_unit label: TSC2 (tuberin) GAP subunit participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TSC2 term: id: UniProtKB:P49815 label: Tuberin role: GAP-domain subunit that stimulates RHEB GTP hydrolysis; the AMPK substrate. function: preferred_term: GTPase activator activity term: id: GO:0005096 label: GTPase activator activity - id: tsc1_unit label: TSC1 (hamartin) stabilising subunit participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TSC1 term: id: UniProtKB:Q92574 label: Hamartin role: Binds and stabilises TSC2 within the complex. function: preferred_term: protein folding chaperone term: id: GO:0044183 label: protein folding chaperone function: preferred_term: GTPase activator activity term: id: GO:0005096 label: GTPase activator activity targets: - preferred_term: RHEB processes: - preferred_term: negative regulation of TORC1 signaling term: id: GO:1904262 label: negative regulation of TORC1 signaling locations: - preferred_term: lysosomal membrane term: id: GO:0005765 label: lysosomal membrane role_description: >- TSC2 GO:0005096 and GO:1904262 are IDA; TSC1 GO:0044183 is IDA. RGD lists TSC1 and its text names Tsc2 as the AMPK target. evidence: - source_id: PMID:14651849 statement: Under energy starvation AMPK phosphorylates TSC2 and enhances its activity, which is needed for translational control and cell-size regulation. supporting_text: Under energy starvation conditions, the AMP-activated protein kinase (AMPK) phosphorylates TSC2 and enhances its activity. - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: RGD text states that AMPK inhibits mTOR signalling by activating Tsc2 and by inhibiting raptor. supporting_text: AMPK inhibits mTOR signaling pathway by activating Tsc2 and downstream of Tsc2 by inhibiting Raptor component of mTOR complex 1 gocam_associations: - model: gomodel:6482692800001813 activity: gomodel:6482692800001813/6482692800001896 title: Inhibition of the canonical mTORC1 signaling following phosphorylation of TSC2 by AMPK in response to glucose starvation (Human) description: TSC2 GTPase activator activity (GO:0005096) on the lysosomal membrane, downstream of AMPK phosphorylation. - model: gomodel:65a1f4f800000922 activity: gomodel:65a1f4f800000922/65a1f4f800000923 title: PELI1 negative regulation of MTOR pathway via TSC1 ubiquitination (Human) description: TSC1 protein folding chaperone (GO:0044183) acting on TSC2. - model: gomodel:65a1f4f800000922 activity: gomodel:65a1f4f800000922/65a1f4f800000942 title: PELI1 negative regulation of MTOR pathway via TSC1 ubiquitination (Human) description: TSC2 GTPase activator activity (GO:0005096) in negative regulation of TORC1 signalling. - order: 5 optional: true role: inhibition of mTORC1 growth signalling node: id: ampk_mtorc1_output label: mTORC1 activation (inhibited by AMPK through TSC2 and raptor) description: >- Included by reference to the mTORC1 activation step of the PI3K-AKT-mTOR module. AMPK opposes it twice: through TSC2 (part 4) and by direct phosphorylation of raptor, which induces 14-3-3 binding. Optional because the module's metabolic outputs do not depend on it. module_ref: pi3k_akt_mtor#mtorc1_activation evidence: - source_id: PMID:18439900 statement: AMPK directly phosphorylates raptor, and this is required for mTORC1 inhibition by energy stress. supporting_text: The phosphorylation of raptor by AMPK is required for the inhibition of mTORC1 and cell-cycle arrest induced by energy stress. - order: 6 optional: true role: inhibition of malonyl-CoA synthesis by AMPK phosphorylation of acetyl-CoA carboxylase node: id: ampk_acc_output label: Acetyl-CoA carboxylase (inhibited by AMPK) description: >- Included by reference to the ACC step of the de novo fatty acid synthesis module. AMPK phosphorylation inhibits ACC and lowers malonyl-CoA, reducing fatty acid synthesis. ACC is a substrate of AMPK, not a participant. module_ref: fatty_acid_de_novo_synthesis#malonyl_coa_synthesis evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: RGD text describes AMPK inhibition of ACC and the resulting fall in malonyl-CoA. supporting_text: Phosphorylation by AMPK inhibits acetyl-CoA carboxylase (ACC) and results in reduced levels of malonyl-CoA product. - order: 7 optional: true role: relief of malonyl-CoA inhibition of carnitine palmitoyltransferase 1 node: id: ampk_cpt1_output label: CPT1 acylcarnitine formation (disinhibited when malonyl-CoA falls) description: >- Included by reference to the CPT1 step of the carnitine shuttle module. Lower malonyl-CoA relieves CPT1 inhibition, so long-chain acyl groups enter mitochondria for beta-oxidation. CPT1A (on the RGD list) is modelled there. module_ref: carnitine_shuttle#cpt1_step evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000542.yaml statement: RGD text describes malonyl-CoA as the CPT1 inhibitor linking ACC to fatty acid oxidation. supporting_text: Importantly, it is also an inhibitor of the carnitine palmitoyl transferase I, required for the transfer of primed cytosolic fatty acids into the mitochondrion where they can undergo degradative beta-oxidation. connections: - source: ampk_upstream_kinases target: ampk_heterotrimer connection_type: POSITIVELY_REGULATES description: LKB1 or CAMKK phosphorylates AMPK alpha Thr172, which is required for activity. - source: ampk_thr172_dephosphorylation target: ampk_heterotrimer connection_type: NEGATIVELY_REGULATES description: Thr172 dephosphorylation switches AMPK off; AMP/ADP binding to gamma protects against it. - source: ampk_heterotrimer target: ampk_tsc_relay connection_type: POSITIVELY_REGULATES description: AMPK phosphorylates TSC2 and enhances TSC1-TSC2 GAP activity. - source: ampk_tsc_relay target: ampk_mtorc1_output connection_type: NEGATIVELY_REGULATES description: TSC1-TSC2 converts RHEB-GTP to RHEB-GDP, preventing mTORC1 activation. - source: ampk_heterotrimer target: ampk_mtorc1_output connection_type: NEGATIVELY_REGULATES description: AMPK phosphorylates raptor, inhibiting mTORC1 independently of TSC2. - source: ampk_heterotrimer target: ampk_acc_output connection_type: NEGATIVELY_REGULATES description: AMPK phosphorylation inhibits acetyl-CoA carboxylase. - source: ampk_acc_output target: ampk_cpt1_output connection_type: NEGATIVELY_REGULATES description: Malonyl-CoA, the ACC product, inhibits CPT1; less malonyl-CoA allows fatty acid entry into mitochondria. knowledge_gaps: - gap_statement: >- Which phosphatase dephosphorylates AMPK alpha Thr172 in a given tissue under physiological energy recovery, and how the AMP/ADP-bound gamma subunit protects the site from each phosphatase class, is not established. boundary: >- PP2A, PPM1E/PPM1F and PP1-R6 have each been implicated by depletion or inhibitor studies in particular cell lines (metal-treated cells, HEK293, MIN6 beta cells), and PPM1F's role is described only as probable. status: OPEN gap_kind: - BIOLOGY significance: >- Determines whether the termination step is one variant per tissue or a redundant set, and which phosphatase is a credible drug target for sustaining AMPK activity. provenance: - reference_id: PMID:20801214 supporting_text: The data indicate that Ppm1E and probably PpM1F are in cellulo AMPK phosphatases and that Ppm1E is a potential anti-diabetic drug target.