PHKA2 encodes the liver isoform of the alpha regulatory subunit of phosphorylase kinase (PhK). PhK is a large hexadecameric (alpha-beta-gamma-delta)4 holoenzyme in which the gamma subunit (PHKG1 in muscle, PHKG2 in liver) is the catalytic serine/threonine kinase and the large alpha (PHKA1/PHKA2) and beta (PHKB) subunits are regulatory; the delta subunit is calmodulin, conferring Ca2+ sensitivity. PHKA2 is itself non-catalytic: as a regulatory subunit it is a target of cAMP-dependent (PKA) phosphorylation which, together with Ca2+/calmodulin, relieves inhibition and activates the catalytic gamma subunit. The activated holoenzyme phosphorylates glycogen phosphorylase (b to a), triggering glycogenolysis; PhK thereby couples hormonal and neural signals to hepatic glycogen breakdown. PHKA2 binds calmodulin and acts in the cytosol. Loss-of-function variants in PHKA2 cause X-linked liver phosphorylase kinase deficiency (glycogen storage disease type IXa, GSD9A), the most common form of PhK deficiency, characterized by hepatomegaly and growth retardation that are usually mild and improve with age.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005964 phosphorylase kinase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred membership in the phosphorylase kinase complex. This is the defining, core cellular-component assignment for PHKA2 as the liver alpha regulatory subunit of the (alpha-beta-gamma-delta)4 holoenzyme. Reason: Strongly supported: PHKA2 is one of the alpha subunits of the phosphorylase kinase holoenzyme. UniProt SUBUNIT describes the complex composition and assigns alpha/beta as regulatory subunits, consistent with this IBA assignment. Supporting Evidence: file:human/PHKA2/PHKA2-uniprot.txt beta, gamma, and delta subunits. Alpha (PHKA1 or PHKA2) and beta (PHKB) |
| GO:0004689 phosphorylase kinase activity | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA electronic assertion that PHKA2 enables phosphorylase kinase activity. This is the activity of the holoenzyme, catalyzed by the gamma subunit (PHKG1/PHKG2); the alpha subunit is regulatory and non-catalytic. Reason: The catalytic phosphorylase kinase activity resides in the gamma subunit, not the alpha regulatory subunit. UniProt states that alpha and beta are regulatory subunits while gamma is the catalytic subunit, so an 'enables' assertion of the holoenzyme kinase activity on PHKA2 over-attributes catalysis to a regulatory chain. PHKA2 contributes to this holoenzyme activity as a complex member (captured in core_functions via contributes_to_molecular_function) but does not independently enable it. Supporting Evidence: file:human/PHKA2/PHKA2-uniprot.txt are regulatory subunits, gamma (PHKG1 or PHKG2) is the catalytic |
| GO:0005516 calmodulin binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based assertion of calmodulin binding. This is a genuine molecular function of the alpha subunit: UniProt notes the alpha chain may bind calmodulin and annotates two calmodulin-binding regions (807-837, 1059-1099). Reason: Well supported and biologically informative for the alpha subunit. Consistent with the Calmodulin-binding keyword and two annotated calmodulin-binding regions. Calmodulin is the delta subunit of the complex, so alpha-CaM binding is functionally central to Ca2+ regulation of the holoenzyme. Supporting Evidence: file:human/PHKA2/PHKA2-uniprot.txt The alpha chain may file:human/PHKA2/PHKA2-uniprot.txt bind calmodulin. |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA electronic assertion of cytoplasmic localization. Correct but non-specific; the more precise, curatorially supported location is the cytosol (GO:0005829). Reason: Cytoplasm is a correct broad parent of the cytosol, where the phosphorylase kinase complex acts on cytosolic glycogen phosphorylase. Retained as a valid, if less specific, location; the cytosol annotation is the more informative one. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Subcellular-location keyword mapping (SL-0039) derived from UniProt's Cell membrane assignment, which is itself an ECO:0000305 (inference from prenylation) annotation, not an experimental localization. Reason: The UniProt Cell membrane / Lipid-anchor location is an ECO:0000305 inference resting on a possible C-terminal farnesyl-cysteine (itself by-similarity, ECO:0000250), with the PTM note stating the terminal tripeptide is 'probably not removed'. The functionally relevant and better-supported compartment is the cytosol, where the complex phosphorylates cytosolic glycogen phosphorylase. Retained but flagged as a weakly supported, likely over-annotated location. Supporting Evidence: file:human/PHKA2/PHKA2-uniprot.txt SUBCELLULAR LOCATION: Cell membrane |
| GO:0005975 carbohydrate metabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based involvement in carbohydrate metabolism. Correct but broad; PHKA2 participates specifically in glycogen catabolism as part of the phosphorylase kinase complex. Reason: Accurate high-level biological-process assignment. The more specific glycogen metabolic / glycogen catabolic terms better capture the function and are reflected in core_functions, but this broad parent is not incorrect. |
| GO:0005977 glycogen metabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Combined-IEA/UniPathway involvement in glycogen metabolism. Accurate: the phosphorylase kinase complex regulates hepatic glycogenolysis, and PHKA2 deficiency causes a glycogen storage disease. Reason: Well aligned with the gene's biology. UniProt PATHWAY records glycogen metabolism, and PHKA2 loss-of-function causes glycogen storage disease type IXa. The catabolic direction is captured more specifically in core_functions. Supporting Evidence: file:human/PHKA2/PHKA2-uniprot.txt PATHWAY: Glycan biosynthesis; glycogen metabolism. |
| GO:0005515 protein binding | IPI PMID:23455922 Interlaboratory reproducibility of large-scale human protein... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a large-scale AP-MS protein-complex interlaboratory reproducibility study. Uninformative term with no specific, functionally interpreted partner recorded. Reason: 'Protein binding' (GO:0005515) is an uninformative molecular-function term. The supporting reference is a high-throughput interactome dataset that does not characterize a specific PHKA2 function; the biologically meaningful partners (PHKG2, PHKB) are already captured by the phosphorylase kinase complex annotation. Per curation policy this experimental IPI is marked as over-annotated rather than removed. |
| GO:0005515 protein binding | IPI PMID:26496610 A human interactome in three quantitative dimensions organiz... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a quantitative human-interactome study. Uninformative term with no specific functional partner recorded. Reason: Uninformative 'protein binding' term derived from a large-scale interactome dataset. No specific PHKA2 function is established. Marked as over-annotated per curation policy rather than removed. |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a large-scale interactome/protein-community study. Uninformative term. Reason: Uninformative 'protein binding' term from a high-throughput interactome dataset; no specific PHKA2 molecular function is established. Marked over-annotated per policy rather than removed. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a binary (Y2H) reference-interactome map. Uninformative term. Reason: Uninformative 'protein binding' term from a large-scale binary interactome screen. No specific, functionally interpreted PHKA2 partner is captured beyond complex membership already annotated elsewhere. Marked over-annotated per policy. |
| GO:0005515 protein binding | IPI PMID:32707033 Kinase Interaction Network Expands Functional and Disease Ro... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a kinase-interaction-network study. The relevant kinase partner (PHKG2, the catalytic gamma subunit) reflects complex membership, but the bare term itself is uninformative. Reason: Uninformative 'protein binding' term. The functionally meaningful interaction (with the catalytic gamma subunit PHKG2) is captured by the phosphorylase kinase complex annotation; the bare MF term adds nothing. Marked over-annotated per policy rather than removed. |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a neurodegenerative-disease interactome mapping study (partner SPRED1). Uninformative term. Reason: Uninformative 'protein binding' term from a high-throughput interactome dataset; the SPRED1 interaction is not functionally interpreted for PHKA2. Marked over-annotated per policy rather than removed. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a proteome-scale, cell-specific interactome study. Uninformative term. Reason: Uninformative 'protein binding' term from a large-scale interactome dataset; no specific PHKA2 function is established. Marked over-annotated per policy. |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from the OpenCell endogenous-tagging cellular cartography study. Uninformative term. Reason: Uninformative 'protein binding' term from a high-throughput cellular-organization dataset; no specific PHKA2 molecular function is established. Marked over-annotated per policy rather than removed. |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | MARK AS OVER ANNOTATED | Summary: Bare protein-binding annotation from a multimodal cell-maps structural/functional genomics study. Uninformative term. Reason: Uninformative 'protein binding' term from a large-scale cell-mapping dataset; no specific PHKA2 function is established. Marked over-annotated per policy rather than removed. |
| GO:0005964 phosphorylase kinase complex | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl-Compara orthology transfer of experimentally verified phosphorylase kinase complex membership. Consistent with the core complex assignment. Reason: Correct and well supported; the same defining complex membership as the IBA and TAS annotations. PHKA2 is the liver alpha regulatory subunit of the holoenzyme. Supporting Evidence: file:human/PHKA2/PHKA2-uniprot.txt Hexadecamer of 4 heterotetramers, each composed of alpha, |
| GO:0005829 cytosol | TAS Reactome:R-HSA-71588 | ACCEPT | Summary: Reactome-curated cytosolic localization. The cytosolic phosphorylase kinase complex phosphorylates cytosolic glycogen phosphorylase (PYGL) in liver. This is the core, functionally relevant location for PHKA2. Reason: Well supported by Reactome curation of the hepatic glycogenolysis reaction; the complex containing PHKA2 acts in the cytosol. This is the preferred location over the by-similarity plasma-membrane assignment. |
| GO:0004689 phosphorylase kinase activity | TAS PMID:7549948 Isolation of cDNA encoding the human liver phosphorylase kin... | MARK AS OVER ANNOTATED | Summary: Author-statement (TAS) assignment of phosphorylase kinase activity from the paper cloning the human liver PHKA2 alpha subunit. The described activity is that of the PhK holoenzyme, catalyzed by the gamma subunit; the alpha subunit is regulatory. Reason: The cited paper isolates and characterizes the liver alpha subunit and discusses liver phosphorylase kinase (the holoenzyme), but the catalytic activity resides in the gamma subunit. Assigning 'enables phosphorylase kinase activity' to the regulatory alpha subunit over-attributes catalysis. PHKA2 contributes to this holoenzyme activity as a complex member (contributes_to_molecular_function in core_functions) but does not independently enable it. Supporting Evidence: PMID:7549948 We isolated and determined the structure of human liver alpha subunit of PHK (PHKA2) cDNA. |
| GO:0005964 phosphorylase kinase complex | TAS PMID:7549948 Isolation of cDNA encoding the human liver phosphorylase kin... | ACCEPT | Summary: Author-statement (TAS) assignment of phosphorylase kinase complex membership from the paper cloning the human liver PHKA2 alpha subunit. Core complex membership. Reason: Directly supported: the reference characterizes PHKA2 as the human liver alpha subunit of phosphorylase kinase, establishing its membership in the holoenzyme complex. Supporting Evidence: PMID:7549948 We isolated and determined the structure of human liver alpha subunit of PHK (PHKA2) cDNA. |
| GO:0005975 carbohydrate metabolic process | TAS PMID:7549948 Isolation of cDNA encoding the human liver phosphorylase kin... | ACCEPT | Summary: Author-statement involvement in carbohydrate metabolism. Correct but broad; the specific process is glycogen catabolism via the phosphorylase kinase complex. Reason: Accurate high-level assignment supported by the paper's framing of PHKA2 in liver glycogenosis. More specific glycogen catabolic terms are captured in core_functions, but this broad parent is not incorrect. Supporting Evidence: PMID:7549948 deficiency is the most frequent liver glycogen storage disease. |
| GO:0006091 generation of precursor metabolites and energy | TAS PMID:7549948 Isolation of cDNA encoding the human liver phosphorylase kin... | KEEP AS NON CORE | Summary: Author-statement involvement in generation of precursor metabolites and energy. This reflects the downstream role of hepatic glycogenolysis in supplying glucose for energy, an indirect/downstream consequence rather than PHKA2's core function. Reason: Glycogenolysis driven by the phosphorylase kinase complex ultimately supplies glucose for energy metabolism, so this term is defensible but represents a downstream physiological role rather than the core molecular/complex function of the regulatory alpha subunit. Retained as non-core. |
| GO:0036211 protein modification process | TAS PMID:7549948 Isolation of cDNA encoding the human liver phosphorylase kin... | MARK AS OVER ANNOTATED | Summary: Author-statement involvement in protein modification process, referring to PhK's phosphorylation of its substrate (glycogen phosphorylase). This is a property of the catalytic gamma subunit and is an over-broad, over-attributed term for the regulatory alpha subunit. Reason: Protein modification is what the holoenzyme's catalytic gamma subunit does (phosphorylating glycogen phosphorylase); assigning it to the non-catalytic alpha regulatory subunit both over-attributes the activity and is uninformatively broad. Marked as over-annotated. Supporting Evidence: file:human/PHKA2/PHKA2-uniprot.txt Phosphorylase b kinase catalyzes the phosphorylation of |
| GO:0005980 glycogen catabolic process | TAS Reactome:R-HSA-71588 | NEW | Summary: Proposed specific biological-process annotation: as a subunit of the cytosolic phosphorylase kinase complex, PHKA2 participates in glycogen catabolism (the complex phosphorylates glycogen phosphorylase to trigger glycogenolysis). Reason: Captures the specific catabolic direction of PHKA2's glycogen-metabolic role, more precise than the existing carbohydrate/glycogen metabolic process annotations. Supported by Reactome curation of the hepatic glycogenolysis reaction catalyzed by the PhK complex containing PHKA2, and by the gene's loss-of-function disease (GSD IXa, a liver glycogenosis). Supporting Evidence: PMID:7549948 deficiency is the most frequent liver glycogen storage disease. |
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Download this section (compressed HTML)Q: Does the C-terminal cysteine of PHKA2 undergo farnesylation in vivo, and if so, does it target a fraction of the complex to membranes, or is the functionally dominant pool cytosolic?
Q: Which specific PKA (and autocatalytic) phosphorylation sites on the PHKA2 alpha subunit mediate activation of the holoenzyme, and how do GSD9A missense variants perturb this regulation versus simply destabilizing the complex?
Experiment: Reconstitute the liver holoenzyme with wild-type versus GSD9A-variant PHKA2 and measure Ca2+/calmodulin- and PKA-phosphorylation-dependent activation of glycogen phosphorylase to distinguish assembly defects from regulatory defects.
Experiment: Determine the subcellular distribution of endogenous PHKA2 in hepatocytes (cytosol versus membrane) and test whether inhibiting prenylation redistributes the complex.
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