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

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.

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.