id: MODULE:protein_kinase_c_signaling title: Protein kinase C signaling — chaperone-assisted maturation, PDPK1 and mTORC2 priming, isoform-class activation by DAG/Ca2+ or the PAR scaffold, RACK1/PICK1 anchoring and PHLPP termination; PRKCA/B/G/D/E/H/Q/Z/I, PDPK1, HSP90AA1/CDC37, PARD3/PARD6, RACK1, PICK1, PHLPP1/2 description: >- The protein kinase C (PKC) family comprises nine human AGC-group serine/threonine kinases, divided into three classes by the second messengers that activate them. All have an N-terminal autoinhibitory pseudosubstrate and a C-terminal kinase domain. Conventional PKCs (PRKCA, PRKCB, PRKCG) have a tandem diacylglycerol (DAG)-binding C1 domain and a calcium-binding C2 domain and need both DAG and Ca2+; novel PKCs (PRKCD, PRKCE, PRKCH, PRKCQ) have a C1 domain with higher DAG affinity and a C2 domain that does not bind calcium, so they need DAG alone; atypical PKCs (PRKCZ, PRKCI) have a single C1 domain that does not bind DAG and are controlled instead by protein-protein interactions, chiefly through the PB1 domain with PAR6 and with PAR3 in the PAR polarity complex. Newly synthesised conventional and novel PKCs are held by the HSP90-CDC37 kinase chaperone while they are processed by three ordered phosphorylations. PDPK1 (PDK1) phosphorylates the activation loop, and then the turn motif and hydrophobic motif in the C-terminal tail are phosphorylated in a step that requires mTORC2. The resulting mature, stable enzyme sits in the cytosol with its pseudosubstrate in the active site. When phospholipase C generates DAG and IP3-released calcium, conventional PKCs are recruited to the plasma membrane by the C2 domain and engage DAG through C1; novel PKCs go to DAG-containing membranes directly. Membrane binding releases the pseudosubstrate, and the active kinase is positioned at particular sites by anchoring proteins, including RACK1, which binds activated PKC, and the PDZ-BAR protein PICK1. The open, active conformation is also sensitive to phosphatases. PHLPP1 and PHLPP2 dephosphorylate the hydrophobic motif, which moves PKC to the detergent-insoluble fraction for degradation and so sets the cellular level of signalling-competent PKC. Atypical PKCs are phosphorylated by PDPK1 in an agonist-dependent manner and, within the PAR3-PAR6-aPKC complex, regulate cell polarity. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0000840 title: protein kinase C (PKC) signaling pathway statement: >- The module boundary follows the RGD Pathway Ontology term and its interactive diagram. The diagram draws Cdc37 and Hsp90aa1 associated with cPKC and nPKC, Pdpk1 positively affecting cPKC, nPKC and aPKC, DAG associated with cPKC and nPKC, Ca2+ associated with cPKC only, Phlpp1 and Phlpp2 negatively affecting cPKC and nPKC, aPKC positively affecting cell polarity, and all three classes associated with a "PKC interactors" node. The upstream Galphaq/PLC-beta/IP3/Ca2+ steps are drawn as links to the subpathways PW:0000229, PW:0001139 and PW:0001140. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0000840.yaml). - source_id: GO:0070528 title: protein kinase C signaling statement: >- The GO mapping recorded for PW:0000840 in the project's module seeds (skos:closeMatch, from the RGD page and PW definition cross-references). - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000840.yaml statement: >- The RGD record text defines the three PKC classes by their responsiveness to DAG and calcium, which is the variant axis of the activation step. supporting_text: A tandem DAG-sensitive C1 domain is present in cPKC and nPKC with the latter group displaying a higher sensitivity. The C2 domain is Ca2+ sensitive in cPKC only. - source_id: PMID:19934406 title: 'Protein kinase C: poised to signal.' statement: >- Review framing the PKC life cycle used for the part order: maturation by phosphorylation, allosteric activation by lipid binding, and downregulation. supporting_text: Cell membranes provide the platform for PKC function, supporting the maturation of PKC through phosphorylation, its allosteric activation by binding specific lipids, and, ultimately, promoting the downregulation of the enzyme. - source_id: PMID:18162466 title: The phosphatase PHLPP controls the cellular levels of protein kinase C. statement: >- Primary paper stating the three ordered maturation phosphorylations and showing that PHLPP-mediated hydrophobic-motif dephosphorylation ends the PKC life cycle. supporting_text: The maturation of PKC requires three ordered phosphorylations, one at the activation loop and two at COOH-terminal sites, the turn motif and the hydrophobic motif, to yield a stable and signaling-competent enzyme. notes: >- Derived from the RGD Pathway Ontology diagram PW:0000840 through the RGD_PATHWAY_ONTOLOGY project's diagram->module route. RGD curates 32 human genes to PW:0000840 (BTK CDC37 COPB1 FSCN1 FYN HSP90AA1 LCK LDB3 PARD3 PARD6A PARD6B PARD6G PCNT PDPK1 PHLPP1 PHLPP2 PICK1 PLCB1-4 PRKCA PRKCB PRKCD PRKCE PRKCG PRKCH PRKCI PRKCQ PRKCZ RACK1 RASA1). Twenty-one are modelled as participants here. The four PLC beta isoforms are covered by reference to another module. Seven are excluded with the reasons below. MTOR, RICTOR and MAPKAP1 (mTORC2) are added although RGD does not list them, because the RGD record text names mTORC2 as required for turn-motif phosphorylation. Boundary decisions. (1) No duplication of the Gq-PLC module. The receptor -> Galphaq -> PLC beta -> IP3/DAG/Ca2+ chain is already modelled in modules/gpcr_plc_calcium_pkc_signaling.yaml. RGD itself draws these steps as links to other pathway diagrams (PW:0000229 Galphaq signalling, PW:0001139/PW:0001140 calcium transport and signalling), not as part of PW:0000840. Second-messenger generation is therefore an optional part included by module_ref to that module's PLC beta node (gpcr_plc_calcium_pkc_signaling#plc_beta_activation). PLCB1-4 are not re-modelled. That part is optional because atypical PKCs need neither DAG nor Ca2+, and because PLC gamma downstream of receptor tyrosine kinases also produces DAG (mentioned in the RGD text but not modelled). The PW ids of the subpathways are mentioned here only and are not evidence source_ids. (2) The core of this module is the PKC life cycle: chaperoned maturation and priming (HSP90-CDC37, PDPK1, mTORC2), isoform-class activation, anchoring and PHLPP termination. The PRKCA node of the Gq-PLC module and the conventional variant here describe the same kinase activity. This module adds the isoform classes and the regulatory machinery around them. (3) The activation step is a variant set on the axis of second-messenger dependence, with selection ONE_OR_MORE because most cells express several classes. Molecular functions follow the experimental GO annotations. Conventional isoforms use calcium,diacylglycerol-dependent serine/threonine kinase activity GO:0004698 (IDA for PRKCA, PRKCB and PRKCG). Novel isoforms use diacylglycerol-dependent, calcium-independent serine/threonine kinase activity GO:0004699 (EXP/IDA for PRKCD, PRKCE and PRKCQ, and the PRKCQ gene-review core function). PRKCH carries GO:0004699 only by IEA, which is noted on its annoton. Atypical isoforms use protein serine/threonine kinase activity GO:0004674 (IDA for PRKCI). GO:0004699 is also IEA/ISS on PRKCI, which is not used because aPKCs do not respond to DAG. PRKCZ carries GO:0004698 by EXP (Reactome-derived), which is inconsistent with its DAG/calcium insensitivity and is flagged as a possible upstream annotation error below. (4) Comparator check for the pathway term. In human GOA, GO:0070528 protein kinase C signaling is carried only by PRKCA and PRKCB (IDA) and PRKCD (IEA). The regulators carry child regulation terms (GO:0090037/GO:0090038 on CD40, DGKQ, EGFR and HSPB1), and PDPK1, HSP90AA1, CDC37, PHLPP1/2, RACK1 and PICK1 carry neither. GO:0070528 is therefore placed only on the module concept and on the PKC kinase annotons. The maturation, anchoring and termination annotons carry their own molecular functions (and protein dephosphorylation for PHLPP) and are not asserted to be involved in GO:0070528. They act on PKC, the enzyme, not on the signal it relays. (5) Maturation. HSP90-CDC37 binding of newly made conventional and novel (not atypical) PKC is modelled as the HSP90-CDC37 chaperone complex GO:1990565. The complex's activity is ATP-dependent protein folding chaperone GO:0140662, the HSP90AA1 gene-review core function. CDC37 is an active unit without its own GO MF, because its only experimental MF rows are protein binding. PDPK1 activation-loop phosphorylation is protein serine/threonine kinase activity GO:0004674 (IDA). It is constitutive for cPKC/nPKC (PMID:9889098) and enhanced by PI 3-kinase products for PRKCZ (PMID:9768361). The mTORC2 step is modelled as the TORC2 complex GO:0031932, with MTOR GO:0004674 and RICTOR/MAPKAP1 enzyme-substrate adaptor activity GO:0140767, as in the human mTORC2 GO-CAM gomodel:66e382fb00001412. The evidence (PMID:18566586, PMID:18566587) shows that mTORC2 is required for turn-motif phosphorylation of conventional PKC and PKCepsilon. RGD states that whether mTORC2 phosphorylates the PKC tail directly is unclear, and this is recorded as a knowledge gap rather than written as a direct kinase-substrate edge on PKC. (6) Atypical PKC and the PAR complex. The PAR3-PAR6 scaffold is modelled inside the atypical variant as a PAR polarity complex (GO:0120157) annoton with signaling adaptor activity GO:0035591, the PARD6B/PARD6G gene-review core function. PARD6A's review uses the parent-adjacent protein-macromolecule adaptor activity GO:0030674. PARD3 has no review and no experimental MF beyond protein binding. Downstream polarity biology (Crumbs and Scribble complexes, apical-basal antagonism) is not modelled. No human or vertebrate polarity module exists in modules/. The closest is modules/dmel_epithelial_polarity_complexes.yaml (Drosophila Par/Crumbs/Scribble), which is not module_ref'd because it is a concrete fly module. A human PAR/Crumbs/Scribble polarity module is a candidate to which the aPKC variant could later point. (7) Anchoring is an optional part with RACK1 and PICK1. These are the two "PKC interactors" with gene reviews, and binding of activated PKC by each is documented (PMID:8302854 for RACK1; PMID:7844141 for PICK1). RACK1 uses its core GO:0060090 molecular adaptor activity. PICK1 uses protein kinase C binding GO:0005080, which its review accepts. PICK1 is also a PKC substrate, so it is kept for its anchoring role only. (8) Exclusions and the substrate-vs-participant rule. FSCN1 (fascin; PKC phosphorylates its actin-binding site) is a PKC substrate and is excluded: it does none of the work of PKC signalling. LDB3 (cypher/ZASP), PCNT (pericentrin) and COPB1 are listed by RGD as "PKC interactors". They are thought to act as compartment-specific anchoring/scaffold proteins (Z-disc, centrosome and Golgi coatomer respectively) but are not modelled, because no cached evidence for the PKC-binding role was assembled here. For COPB1 the coatomer RACK literature may refer to the beta-prime subunit (COPB2) rather than beta-COP. This was not verified and is recorded only as a question for RGD. BTK, LCK and FYN are tyrosine kinases with reciprocal cross-talk with PKC (tyrosine phosphorylation of novel PKCs, PKC phosphorylation of BTK). RASA1 (p120 RasGAP) is a Ras regulator. Both groups belong to antigen-receptor and Ras modules, not to the PKC life cycle. Under the CLAUDE.md rule, kinases that modify PKC or are modified by it do not get PKC-signalling participation unless they perform a step of the PKC module itself. (9) Signal termination by DGK conversion of DAG to phosphatidic acid and by receptor internalisation is mentioned by RGD as "not shown" and is not modelled. HSP70-mediated rephosphorylation and recycling of dephosphorylated PKC (RGD text) is described in prose only. Downstream outcomes drawn by RGD (proliferation, differentiation, cell death) are out of scope. Possible upstream errors noticed: the RGD PW:0000840 text says "Pdpk1 phosphorylates the activation loop of PLC", where PKC is plainly meant. PRKCZ (Q05513) carries GO:0004698 calcium,diacylglycerol-dependent serine/threonine kinase activity by EXP, which contradicts aPKC insensitivity to DAG and calcium. GO-CAM coverage is linked under gocam_associations for PRKCA, PRKCG (the project's best-overlap model gomodel:66b5638000002273), PRKCI, PDPK1/mTORC2 and PHLPP1. No GO-CAM in gocams/index.tsv covers PRKCB, PRKCD, PRKCE, PRKCH, PRKCQ, PRKCZ, HSP90AA1, CDC37, RACK1, PICK1, PARD3/PARD6 or PHLPP2. Gene reviews exist for HSP90AA1, PARD6A, PARD6B, PARD6G, PICK1, PRKCQ and RACK1, and their core functions were used. The other members have no review yet. PANTHER family ids and PTNs are deliberately not asserted. module: id: protein_kinase_c_signaling label: Protein kinase C signaling module_type: SIGNALING_PATHWAY concepts: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling description: >- The GO term mapped to PW:0000840: intracellular signalling mediated by activated PKC isoforms. context: taxa: - preferred_term: Homo sapiens term: id: NCBITaxon:9606 label: Homo sapiens cellular_components: - preferred_term: cytosol term: id: GO:0005829 label: cytosol - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane parts: - order: 1 role: chaperone-assisted maturation and priming phosphorylation of newly synthesised PKC node: id: pkc_maturation label: HSP90-CDC37 chaperoning, PDPK1 activation-loop and mTORC2-dependent C-tail phosphorylation module_type: REGULATORY_STEP description: >- Newly made conventional and novel PKCs bind HSP90-CDC37 through a C-tail PXXP clamp. PDPK1 then phosphorylates the activation loop, and the turn and hydrophobic motifs are phosphorylated in an mTORC2-dependent step. Without these steps PKC is inactive and unstable. Atypical PKCs do not bind HSP90-CDC37, and their PDPK1 phosphorylation depends on agonist. parts: - order: 1 role: kinase-specific chaperoning of nascent cPKC/nPKC node: id: pkc_hsp90_cdc37_chaperoning label: HSP90-CDC37 holds newly synthesised PKC for processing module_type: PROTEIN_COMPLEX annotons: - id: hsp90_cdc37_pkc_chaperone label: HSP90-CDC37 kinase chaperone complex participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: HSP90-CDC37 chaperone complex term: id: GO:1990565 label: HSP90-CDC37 chaperone complex active_units: - id: hsp90aa1_unit label: HSP90alpha ATPase chaperone participant: selector_type: GENE_PRODUCT gene_product: preferred_term: HSP90AA1 term: id: UniProtKB:P07900 label: Heat shock protein HSP 90-alpha role: ATP-driven clamp that stabilises the kinase client. function: preferred_term: ATP-dependent protein folding chaperone term: id: GO:0140662 label: ATP-dependent protein folding chaperone - id: cdc37_unit label: CDC37 kinase-targeting co-chaperone participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CDC37 term: id: UniProtKB:Q16543 label: Hsp90 co-chaperone Cdc37 role: >- Recruits kinase clients to HSP90; no experimental GO molecular function other than protein binding is recorded. function: preferred_term: ATP-dependent protein folding chaperone term: id: GO:0140662 label: ATP-dependent protein folding chaperone processes: - preferred_term: protein maturation term: id: GO:0051604 label: protein maturation locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Required for processing phosphorylation of conventional and novel PKC. Matches the HSP90AA1 gene-review core function for HSP90-CDC37 kinase chaperoning. evidence: - source_id: PMID:19091746 statement: >- Conventional and novel, but not atypical, PKCs bind HSP90 and CDC37 through the C-tail PXXP motif, and inhibiting either chaperone slows PKC processing phosphorylation. supporting_text: Co-immunoprecipitation studies reveal that conventional and novel, but not atypical, PKC isozymes bind the chaperones Hsp90 and Cdc37 through a PXXP-dependent mechanism. Inhibitors of Hsp90 and Cdc37 significantly reduce the rate of processing phosphorylation of PKC. - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000840.yaml statement: RGD draws Hsp90aa1 and Cdc37 associated with cPKC and nPKC. supporting_text: The Hsp90 chaperone and Cdc37co-chaperone are required for the proper processing of cPKC and nPKCs. - order: 2 role: activation-loop phosphorylation by PDPK1 node: id: pkc_pdpk1_priming label: PDPK1 phosphorylates the PKC activation loop module_type: REACTION annotons: - id: pdpk1_pkc_activation_loop label: PDPK1 activation-loop kinase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PDPK1 term: id: UniProtKB:O15530 label: 3-phosphoinositide-dependent protein kinase 1 function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity substrates: - preferred_term: activation-loop threonine of newly synthesised PKC (Thr500 in PKCbetaII, Thr410 in PKCzeta) locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- First step of PKC processing: the activation-loop phosphate allows the C-terminal phosphorylations that follow. Constitutive for cPKC/nPKC and PI 3-kinase-enhanced for atypical PKC zeta. evidence: - source_id: PMID:9889098 statement: PDPK1 directly phosphorylates the activation loop of conventional PKC, the first step of its maturation. supporting_text: Studies performed in vitro establish that PDK-1 directly phosphorylates PKC on the activation loop, thereby allowing carboxy-terminal phosphorylation of PKC. - source_id: PMID:9768361 statement: PDPK1 phosphorylates Thr410 in the PKC zeta activation loop in a PIP3-enhanced manner. supporting_text: PDK-1 phosphorylates and activates PKC zeta in vivo, and we have shown that this is due to phosphorylation of threonine 410 in the PKC zeta activation loop. gocam_associations: - model: gomodel:66e382fb00001412 activity: gomodel:66e382fb00001412/66e382fb00001447 title: mTORC2 signaling (Human). description: >- PDPK1 protein serine/threonine kinase activity (GO:0004674) in the mTORC2 model; the model's substrate is AKT1 rather than PKC. - order: 3 role: mTORC2-dependent turn-motif and hydrophobic-motif phosphorylation node: id: pkc_mtorc2_ctail label: mTORC2-dependent phosphorylation of the PKC C-terminal tail module_type: REGULATORY_STEP description: >- Phosphorylation of the turn motif and the hydrophobic motif completes maturation and stabilises conventional and novel PKC. mTORC2 is required for it. Whether mTORC2 phosphorylates the PKC tail directly or acts through another kinase or autophosphorylation is unresolved (see knowledge gaps). annotons: - id: mtorc2_pkc_ctail label: mTORC2 kinase complex participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: mTORC2 term: id: GO:0031932 label: TORC2 complex active_units: - id: mtor_unit label: mTOR catalytic subunit participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MTOR term: id: UniProtKB:P42345 label: Serine/threonine-protein kinase mTOR role: Catalytic kinase subunit. function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity - id: rictor_unit label: RICTOR substrate adaptor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RICTOR term: id: UniProtKB:Q6R327 label: Rapamycin-insensitive companion of mTOR role: mTORC2-defining subunit that presents substrates to mTOR. function: preferred_term: enzyme-substrate adaptor activity term: id: GO:0140767 label: enzyme-substrate adaptor activity - id: mapkap1_unit label: SIN1 (MAPKAP1) substrate adaptor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MAPKAP1 (SIN1) term: id: UniProtKB:Q9BPZ7 label: Target of rapamycin complex 2 subunit MAPKAP1 role: mTORC2 subunit required for substrate recognition. function: preferred_term: enzyme-substrate adaptor activity term: id: GO:0140767 label: enzyme-substrate adaptor activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Required for turn-motif (and, for PKCalpha, hydrophobic-motif) phosphorylation of newly synthesised PKC. No complex-level MF is asserted, because it is not settled that mTORC2 phosphorylates PKC directly. evidence: - source_id: PMID:18566587 statement: >- mTORC2 is needed for turn- and hydrophobic-motif phosphorylation of all conventional PKCs and PKCepsilon. Turn-motif phosphorylation is essential for PKCalpha maturation. supporting_text: Here, we show that the mammalian target of rapamycin complex 2 (mTORC2) has an important function in phosphorylation of both TM and HM in all conventional PKCs, novel PKCepsilon as well as Akt. - source_id: PMID:18566586 statement: mTOR, SIN1 and RICTOR are required for conventional PKC turn-motif phosphorylation. supporting_text: Here, we demonstrate that mTOR, SIN1 and rictor, components of mammalian (m)TORC2, are required for phosphorylation of Akt and conventional protein kinase C (PKC) at the turn motif (TM) site. - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000840.yaml statement: RGD text names mTORC2 but leaves its directness open; mTORC2 is not on the RGD gene list. supporting_text: Whether the role of mTORC2 is direct or indirect, via activation of an upstream kinase, is currently unclear. gocam_associations: - model: gomodel:66e382fb00001412 activity: gomodel:66e382fb00001412/66e382fb00001413 title: mTORC2 signaling (Human). description: >- MTOR protein serine/threonine kinase activity (GO:0004674) with RICTOR (66e382fb00001432) and MAPKAP1 (66e382fb00001422) as enzyme-substrate adaptors; the modelled substrate is AKT1, not PKC. connections: - source: pkc_hsp90_cdc37_chaperoning target: pkc_pdpk1_priming connection_type: PRECEDES description: Chaperone binding of nascent PKC is required for its processing phosphorylation. - source: pkc_pdpk1_priming target: pkc_mtorc2_ctail connection_type: PRECEDES description: The activation-loop phosphate allows the C-terminal phosphorylations. chaining_status: NOT_APPLICABLE chaining_note: Sequential protein phosphorylations on PKC; no CoA intermediate. - order: 2 optional: true role: generation of the DAG and Ca2+ second messengers node: id: pkc_second_messenger_generation label: PLC beta hydrolysis of PIP2 to DAG and IP3 (shared Gq effector) description: >- Included by reference to the PLC beta step of the Gq-PLC-calcium-PKC module. The IP3-receptor calcium release that follows is in the same module. Optional, because atypical PKCs do not use these messengers and other DAG sources (PLC gamma, phospholipase D/phosphatidate phosphatase) can substitute. module_ref: gpcr_plc_calcium_pkc_signaling#plc_beta_activation - order: 3 role: second-messenger or scaffold activation of mature PKC, by isoform class node: id: pkc_isoform_activation label: Activation of mature PKC isoforms module_type: SIGNALING_PATHWAY description: >- The mature, autoinhibited kinase is opened when its regulatory domains engage membrane lipids or partner proteins. The isoform class determines what is needed. variant_sets: - id: pkc_isoform_class label: PKC isoform class axis: second-messenger dependence (DAG plus Ca2+, DAG only, or neither) selection: ONE_OR_MORE notes: >- Most cell types express members of more than one class; the classes differ in regulatory domains, not in kinase-domain chemistry. evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000840.yaml statement: RGD text describes the atypical class as DAG-insensitive and regulated by other lipids or protein partners. supporting_text: this group depends on other lipids or protein-protein interactions for functional regulation variants: - id: conventional_pkc label: Conventional PKC (DAG- and Ca2+-dependent) module_type: SIGNALING_PATHWAY description: >- PRKCA, PRKCB and PRKCG. A Ca2+ rise moves the C2 domain to plasma-membrane phosphatidylserine/PIP2, and the C1 domain then binds DAG, releasing the pseudosubstrate. annotons: - id: prkca_kinase label: PKC alpha participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCA term: id: UniProtKB:P17252 label: Protein kinase C alpha type function: preferred_term: calcium,diacylglycerol-dependent serine/threonine kinase activity term: id: GO:0004698 label: calcium,diacylglycerol-dependent serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: Ubiquitous conventional isoform; GO:0004698 and GO:0070528 are IDA in GOA. gocam_associations: - model: gomodel:6438950a00000766 activity: gomodel:6438950a00000766/6438950a00000816 title: Ubiquitination of WNK4 in the distal nephron by KLHL3 and its regulation by phosphorylation and dephosphorylation (Human) description: PRKCA calcium,diacylglycerol-dependent serine/threonine kinase activity (GO:0004698) acting on KLHL3. - model: gomodel:69c59f8a00000079 activity: gomodel:69c59f8a00000079/69c59f8a00000109 title: Negative regulation of DRD1-mediated signaling following phosphorylation by PKC (Human). description: PRKCA GO:0004698 phosphorylating DRD1 in negative regulation of dopamine receptor signalling. - id: prkcb_kinase label: PKC beta participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCB term: id: UniProtKB:P05771 label: Protein kinase C beta type function: preferred_term: calcium,diacylglycerol-dependent serine/threonine kinase activity term: id: GO:0004698 label: calcium,diacylglycerol-dependent serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Conventional isoform (betaI/betaII splice forms); PKCbetaII is the model substrate in the HSP90-CDC37, PDPK1 and PHLPP studies cited here. - id: prkcg_kinase label: PKC gamma participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCG term: id: UniProtKB:P05129 label: Protein kinase C gamma type function: preferred_term: calcium,diacylglycerol-dependent serine/threonine kinase activity term: id: GO:0004698 label: calcium,diacylglycerol-dependent serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: Neuron-restricted conventional isoform (cerebellar Purkinje cells, spinal dorsal horn). gocam_associations: - model: gomodel:66b5638000002273 activity: gomodel:66b5638000002273/66b5638000002312 title: GRIM1 activates GRID2 via GNAQ in Purkinje cells (Human). description: >- PRKCG GO:0004698 downstream of GNAQ and PLCB3 in GO:0007200; the project's best-overlap GO-CAM for PW:0000840. evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000840.yaml statement: Only the conventional class has a calcium-sensing C2 domain; RGD draws Ca2+ associated with cPKC alone. supporting_text: The C2 domain is Ca2+ sensitive in cPKC only. - id: novel_pkc label: Novel PKC (DAG-dependent, Ca2+-independent) module_type: SIGNALING_PATHWAY description: >- PRKCD, PRKCE, PRKCH and PRKCQ. Their C2-like domain does not bind calcium. A higher-affinity C1 domain recruits them directly to DAG-containing membranes. annotons: - id: prkcd_kinase label: PKC delta participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCD term: id: UniProtKB:Q05655 label: Protein kinase C delta type function: preferred_term: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity term: id: GO:0004699 label: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Novel isoform; GO:0004699 is EXP in GOA. GOA also holds an IDA row for GO:0004698, which is not used because the C2 domain of PKCdelta does not bind calcium. - id: prkce_kinase label: PKC epsilon participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCE term: id: UniProtKB:Q02156 label: Protein kinase C epsilon type function: preferred_term: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity term: id: GO:0004699 label: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: Novel isoform; GO:0004699 is IDA in GOA; mTORC2-dependent C-tail processing is shown for PKCepsilon. - id: prkch_kinase label: PKC eta participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCH term: id: UniProtKB:P24723 label: Protein kinase C eta type function: preferred_term: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity term: id: GO:0004699 label: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Novel isoform, mainly epithelial. GO:0004699 is IEA only for PRKCH; its experimental kinase rows are GO:0004672/GO:0106310. Class membership supports the assignment. - id: prkcq_kinase label: PKC theta participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCQ term: id: UniProtKB:Q04759 label: Protein kinase C theta type function: preferred_term: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity term: id: GO:0004699 label: diacylglycerol-dependent, calcium-independent serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Novel isoform of T cells and platelets; GO:0004699 is the core function in the PRKCQ gene review (immunological-synapse TCR signalling). evidence: - source_id: file:human/PRKCQ/PRKCQ-uniprot.txt statement: UniProt curated activity regulation places PRKCQ with the calcium-insensitive, DAG-activated novel PKCs. supporting_text: Novel PKCs (PRKCD, PRKCE, PRKCH and PRKCQ) are calcium-insensitive, but activated by diacylglycerol (DAG) and phosphatidylserine. evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000840.yaml statement: RGD draws DAG, not Ca2+, associated with nPKC, and notes the higher DAG sensitivity of the novel class. supporting_text: A tandem DAG-sensitive C1 domain is present in cPKC and nPKC with the latter group displaying a higher sensitivity. - id: atypical_pkc label: Atypical PKC (DAG- and Ca2+-independent; PAR3-PAR6 scaffold) module_type: SIGNALING_PATHWAY description: >- PRKCZ and PRKCI. Their single atypical C1 domain does not bind DAG and they lack a C2 domain. Activity and localisation are controlled by PB1-mediated binding to PAR6, which links them to CDC42-GTP and PAR3, and by agonist-dependent PDPK1 phosphorylation. Within the PAR complex, aPKC phosphorylates polarity substrates that set apical-basal membrane identity. annotons: - id: prkcz_kinase label: PKC zeta participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCZ term: id: UniProtKB:Q05513 label: Protein kinase C zeta type function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Atypical isoform; GO:0004674 is IDA in GOA (PMID:15069075). An EXP GO:0004698 (Ca2+/DAG-dependent) row in GOA conflicts with its class and is not used. evidence: - source_id: PMID:9768361 statement: Membrane-targeted PKC zeta is constitutively active, consistent with regulation by localisation rather than by DAG. supporting_text: Consistent with the notion that PKCs are enzymes that are regulated at the plasma membrane, a membrane-targeted PKC zeta is constitutively active in the absence of agonist stimulation. - id: prkci_kinase label: PKC iota/lambda participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKCI term: id: UniProtKB:P41743 label: Protein kinase C iota type function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity processes: - preferred_term: protein kinase C signaling term: id: GO:0070528 label: protein kinase C signaling locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Atypical isoform and the principal aPKC of the epithelial PAR complex; GO:0004674 is IDA in GOA. gocam_associations: - model: gomodel:64d5781900002033 activity: gomodel:64d5781900002033/64d5781900002041 title: Insulin-mediated activation of the ARF6-RAC1 axis in neurite outgrowth (Human) description: PRKCI protein serine/threonine kinase activity (GO:0004674) in positive regulation of neuron projection development. - id: par3_par6_scaffold label: PAR3-PAR6 polarity scaffold participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: PAR polarity complex (PAR3-PAR6 scaffold for aPKC) term: id: GO:0120157 label: PAR polarity complex active_units: - id: pard3_unit label: PAR3 multi-PDZ scaffold participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PARD3 term: id: UniProtKB:Q8TEW0 label: Partitioning defective 3 homolog role: >- Binds PAR6 through its PDZ domains and binds aPKC independently; also an aPKC substrate and inhibitor in vitro. - id: pard6_unit label: PAR6 adaptor (PARD6A, PARD6B or PARD6G) participant: selector_type: FAMILY family: preferred_term: PAR6 family (PARD6A/PARD6B/PARD6G) representative_members: - preferred_term: PARD6A term: id: UniProtKB:Q9NPB6 label: Partitioning defective 6 homolog alpha - preferred_term: PARD6B term: id: UniProtKB:Q9BYG5 label: Partitioning defective 6 homolog beta - preferred_term: PARD6G term: id: UniProtKB:Q9BYG4 label: Partitioning defective 6 homolog gamma role: >- PB1-domain partner of aPKC; links aPKC to CDC42-GTP through its semi-CRIB motif and to PAR3 through its PDZ domain. function: preferred_term: signaling adaptor activity term: id: GO:0035591 label: signaling adaptor activity function: preferred_term: signaling adaptor activity term: id: GO:0035591 label: signaling adaptor activity locations: - preferred_term: apical plasma membrane term: id: GO:0016324 label: apical plasma membrane role_description: >- Scaffold that localises and controls atypical PKC in place of the DAG and Ca2+ inputs used by the other classes; signaling adaptor activity is the core function in the PARD6B and PARD6G gene reviews. evidence: - source_id: PMID:10934474 statement: PAR6 links CDC42 and atypical PKC to PAR3. supporting_text: Thus, Par6 is a key adaptor that links Cdc42 and atypical PKCs to Par3. - source_id: PMID:10934475 statement: PAR3 and PAR6 each bind aPKC and act as scaffolds; PAR3 is an aPKC substrate and inhibitor in vitro. supporting_text: mPAR-6 binds to Cdc42/Rac1 GTPases, and mPAR-3 and mPAR-6 bind independently to atypical protein kinase C (aPKC) isoforms. In vitro, mPAR-3 acts as a substrate and an inhibitor of aPKC. connections: - source: par3_par6_scaffold target: prkci_kinase connection_type: POSITIVELY_REGULATES description: The PAR3-PAR6 scaffold localises and controls aPKC at the apical cortex and tight junctions. - source: par3_par6_scaffold target: prkcz_kinase connection_type: POSITIVELY_REGULATES description: PAR6 binds PKC zeta through the PB1 domain in the same way. - order: 4 optional: true role: anchoring of activated PKC at subcellular sites node: id: pkc_anchoring label: Anchoring of activated PKC by RACK1 and PICK1 module_type: REGULATORY_STEP description: >- After activation, PKC is held near particular substrates by binding proteins. RACK1 binds activated PKC (classically PKCbetaII), and the PDZ-BAR protein PICK1 binds the PKCalpha catalytic domain and targets it to PICK1 cargo such as AMPA receptors. Other compartment-specific anchors (for example pericentrin, cypher/ZASP and coatomer) are noted in the module notes but not modelled. Optional, because PKC signals without them. annotons: - id: rack1_pkc_anchor label: RACK1 receptor for activated C kinase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RACK1 term: id: UniProtKB:P63244 label: Small ribosomal subunit protein RACK1 function: preferred_term: molecular adaptor activity term: id: GO:0060090 label: molecular adaptor activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- WD40 scaffold that binds activated, not inactive, PKC. Molecular adaptor activity is its signalling-scaffold core function in the RACK1 gene review. Protein kinase C binding GO:0005080 (IDA) is retained there as non-core. evidence: - source_id: PMID:8302854 statement: RACK1 binds PKC only in the presence of PKC activators, saturably and specifically. supporting_text: RACK1 bound PKC in the presence of PKC activators, but not in their absence. - id: pick1_pkc_anchor label: PICK1 PDZ-BAR PKC-binding scaffold participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PICK1 term: id: UniProtKB:Q9NRD5 label: PRKCA-binding protein function: preferred_term: protein kinase C binding term: id: GO:0005080 label: protein kinase C binding locations: - preferred_term: postsynaptic density term: id: GO:0014069 label: postsynaptic density role_description: >- Binds the catalytic domain of activated PKCalpha and couples it to PDZ-bound cargo. It is also a PKC substrate; it is modelled here for its anchoring role only. GO:0005080 is accepted in the PICK1 gene review. evidence: - source_id: PMID:7844141 statement: PICK1 was isolated as a protein that binds the catalytic domain of activated PKCalpha and is phosphorylated by it. supporting_text: One of these proteins, designated PICK1, interacts specifically with the catalytic domain of PKC and is an efficient substrate for phosphorylation by PKC in vitro and in vivo. - order: 5 role: termination by hydrophobic-motif dephosphorylation and degradation node: id: pkc_phlpp_termination label: PHLPP1/PHLPP2 dephosphorylate the PKC hydrophobic motif module_type: REGULATORY_STEP description: >- In the open, membrane-bound conformation, the PKC hydrophobic motif is accessible to the PP2C-family phosphatases PHLPP1 and PHLPP2. Dephosphorylation moves PKC to the detergent-insoluble fraction, where it is further dephosphorylated and degraded, which sets the steady-state level of conventional and novel PKC. annotons: - id: phlpp1_pkc_dephosphorylation label: PHLPP1 hydrophobic-motif phosphatase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PHLPP1 term: id: UniProtKB:O60346 label: PH domain leucine-rich repeat-containing protein phosphatase 1 function: preferred_term: protein serine/threonine phosphatase activity term: id: GO:0004722 label: protein serine/threonine phosphatase activity processes: - preferred_term: protein dephosphorylation term: id: GO:0006470 label: protein dephosphorylation locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Dephosphorylates the hydrophobic motif of PKCbetaII and PKCalpha; GO:0004722 is IDA/EXP in GOA. evidence: - source_id: PMID:18162466 statement: PHLPP1 and PHLPP2 dephosphorylate the PKCbetaII hydrophobic motif, ending the PKC life cycle. supporting_text: Here we show that the two PHLPP isoforms, PHLPP1 and PHLPP2, also dephosphorylate the hydrophobic motif on PKC betaII, an event that shunts PKC to the detergent-insoluble fraction, effectively terminating its life cycle. - source_id: PMID:18162466 statement: Loss of PHLPP raises the levels of conventional and novel PKC. supporting_text: Last, we show that depletion of PHLPP in colon cancer and normal breast epithelial cells results in an increase in conventional and novel PKC levels. gocam_associations: - model: gomodel:65a1f4f800000029 activity: gomodel:65a1f4f800000029/65a1f4f800000050 title: USP49 and SIRT7 inhibition of AKT1 via PHLPP1-mediated dephosphorylation of AKT1 (Human) description: >- PHLPP1 protein serine/threonine phosphatase activity (GO:0004722); the modelled substrate is AKT1, the hydrophobic-motif paralogue of the PKC site. - id: phlpp2_pkc_dephosphorylation label: PHLPP2 hydrophobic-motif phosphatase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PHLPP2 term: id: UniProtKB:Q6ZVD8 label: PH domain leucine-rich repeat-containing protein phosphatase 2 function: preferred_term: protein serine/threonine phosphatase activity term: id: GO:0004722 label: protein serine/threonine phosphatase activity processes: - preferred_term: protein dephosphorylation term: id: GO:0006470 label: protein dephosphorylation locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: PHLPP paralogue with the same hydrophobic-motif activity on PKC; GO:0004722 is EXP in GOA. evidence: - source_id: PMID:18162466 statement: PHLPP2 also dephosphorylates the PKC hydrophobic motif. supporting_text: Here we show that the two PHLPP isoforms, PHLPP1 and PHLPP2, also dephosphorylate the hydrophobic motif on PKC betaII connections: - source: pkc_maturation target: pkc_isoform_activation connection_type: PRECEDES description: >- Only mature, fully phosphorylated PKC can be activated by second messengers. For atypical PKC, PDPK1 phosphorylation is agonist-dependent rather than a prior step. chaining_status: NOT_APPLICABLE chaining_note: Protein maturation preceding allosteric activation; no metabolite intermediate. - source: pkc_pdpk1_priming target: atypical_pkc connection_type: POSITIVELY_REGULATES description: PDPK1 phosphorylates the atypical PKC activation loop (PKC zeta Thr410), enhanced by PI 3-kinase products. - source: pkc_second_messenger_generation target: conventional_pkc connection_type: POSITIVELY_REGULATES description: DAG plus IP3-released Ca2+ recruit and activate conventional PKC. - source: pkc_second_messenger_generation target: novel_pkc connection_type: POSITIVELY_REGULATES description: DAG alone recruits and activates novel PKC. - source: pkc_anchoring target: pkc_isoform_activation connection_type: POSITIVELY_REGULATES description: Anchoring proteins hold activated PKC near its substrates. - source: pkc_phlpp_termination target: conventional_pkc connection_type: NEGATIVELY_REGULATES description: Hydrophobic-motif dephosphorylation sends conventional PKC to degradation. - source: pkc_phlpp_termination target: novel_pkc connection_type: NEGATIVELY_REGULATES description: PHLPP depletion raises novel as well as conventional PKC levels. knowledge_gaps: - gap_statement: >- It is unresolved whether mTORC2 itself phosphorylates the PKC turn motif and hydrophobic motif, or whether it acts indirectly, for example by enabling autophosphorylation of the C-terminal tail or by activating another kinase. boundary: >- Genetic ablation of RICTOR, SIN1 or mTOR abolishes PKCalpha turn-motif phosphorylation and blocks maturation, and mTORC2 can phosphorylate the corresponding Akt sites in vitro. Direct mTORC2 phosphorylation of the PKC turn motif in vitro has not been established in the cited work. status: OPEN gap_kind: - BIOLOGY significance: >- Determines whether mTORC2 is drawn as a kinase acting on PKC or as an indirect requirement, and so whether mTORC2 inhibitors act on PKC by removing a direct priming step. provenance: - reference_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000840.yaml supporting_text: Whether the role of mTORC2 is direct or indirect, via activation of an upstream kinase, is currently unclear. - reference_id: PMID:18566587 supporting_text: Ablation of mTORC2 components (Rictor, Sin1 or mTOR) abolished phosphorylation on the TM of both PKCalpha and Akt and HM of Akt and decreased HM phosphorylation of PKCalpha. - gap_statement: >- How atypical PKCs become catalytically competent without HSP90-CDC37 and without DAG, and whether PDPK1 phosphorylation of aPKC is truly agonist-gated in vivo or constitutive, is not settled. boundary: >- Atypical PKCs do not co-immunoprecipitate with HSP90-CDC37, and PDPK1 phosphorylates PKC zeta Thr410 in a PIP3-enhanced manner, but the maturation route of the aPKC tail is not defined. status: OPEN gap_kind: - BIOLOGY significance: >- The atypical variant's maturation sub-step cannot be modelled with confidence, so the module draws only the shared PDPK1 input for aPKC. provenance: - reference_id: PMID:19091746 supporting_text: Co-immunoprecipitation studies reveal that conventional and novel, but not atypical, PKC isozymes bind the chaperones Hsp90 and Cdc37 through a PXXP-dependent mechanism.