PHKA1 is the skeletal-muscle isoform of the alpha regulatory subunit ("alpha M") of phosphorylase kinase (PhK), a large (alpha-beta-gamma-delta)4 hexadecameric holoenzyme of glycogen metabolism. Within PhK the gamma subunit (PHKG1/PHKG2) is the catalytic protein kinase, while the alpha (PHKA1/PHKA2) and beta (PHKB) subunits are large, non-catalytic regulatory subunits and the delta subunit is calmodulin. The alpha subunit possesses a glucoamylase-like fold but has no detectable catalytic activity; it bridges the beta subunit to the gamma-delta catalytic subcomplex and holds the gamma subunit in an autoinhibited state. PhK is switched on by cAMP-dependent protein kinase (PKA) phosphorylation of serine residues in the alpha and beta subunits together with Ca2+/calmodulin, which relieves autoinhibition and activates the catalytic gamma subunit. Activated PhK phosphorylates glycogen phosphorylase (converting the inactive b form to the active a form), triggering glycogenolysis; in muscle this supplies glucose-1-phosphate for glycolytic ATP production during contraction. PHKA1 can also bind calmodulin directly. The protein is cytosolic. Loss-of-function variants in PHKA1 cause X-linked glycogen storage disease type IXd (GSD9D, muscle phosphorylase kinase deficiency), presenting with exercise intolerance, myalgia, cramps and occasional myoglobinuria.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005964 phosphorylase kinase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) annotation placing PHKA1 as a subunit of the phosphorylase kinase complex. This is well supported: PHKA1 is the alpha regulatory subunit of the PhK (alpha-beta-gamma-delta)4 holoenzyme, confirmed by cryo-EM of the human muscle complex. Reason: Complex membership is a core, correct annotation for PHKA1. The alpha subunit is an integral, structurally defined component of the phosphorylase kinase holoenzyme. Supporting Evidence: PMID:38548794 The 1.3-megadalton PhK Ξ±4Ξ²4Ξ³4Ξ΄4 hexadecamer consists of a tetramer of tetramer, wherein four Ξ±Ξ²Ξ³Ξ΄ modules are connected by the central Ξ²4 scaffold. file:human/PHKA1/PHKA1-uniprot.txt Alpha (PHKA1 or PHKA2) and beta (PHKB) CC are regulatory subunits, gamma (PHKG1 or PHKG2) is the catalytic CC subunit, and delta is calmodulin. |
| GO:0004689 phosphorylase kinase activity | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA electronic annotation asserting that PHKA1 "enables" phosphorylase kinase activity. Phosphorylase kinase activity is a property of the intact PhK holoenzyme, and the catalytic protein kinase is the gamma subunit (PHKG1/PHKG2). PHKA1 is a non-catalytic regulatory subunit; the cryo-EM structure shows the alpha subunit has a glucoamylase-like fold but no detectable enzyme activity. Reason: Annotating PHKA1 with "enables phosphorylase kinase activity" at the protein level over-attributes the holoenzyme's catalytic activity to a regulatory subunit that is itself not a kinase. The activity is better captured as a contribution to the complex (see core_functions contributes_to_molecular_function), not as an activity PHKA1 independently enables. Supporting Evidence: PMID:38548794 The Ξ±- and Ξ²-subunits possess glucoamylase-like domains, but exhibit no detectable enzyme activities. file:human/PHKA1/PHKA1-uniprot.txt Alpha (PHKA1 or PHKA2) and beta (PHKB) CC are regulatory subunits, gamma (PHKG1 or PHKG2) is the catalytic CC subunit, and delta is calmodulin. |
| GO:0005516 calmodulin binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO electronic annotation of calmodulin binding. The alpha subunit is described as able to bind calmodulin, and UniProt annotates two predicted calmodulin-binding regions (residues 810-840 and 1046-1086). Calmodulin is also the delta subunit of the holoenzyme, and Ca2+/calmodulin is central to PhK regulation. Reason: Calmodulin binding is a plausible and biologically meaningful molecular function of the alpha regulatory subunit, consistent with UniProt annotation and the Ca2+/calmodulin regulation of the complex. Supporting Evidence: file:human/PHKA1/PHKA1-uniprot.txt Phosphorylase b kinase catalyzes the phosphorylation of CC serine in certain substrates, including troponin I. The alpha chain may CC bind calmodulin. |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA electronic annotation to the broad cytoplasm term. PhK is a cytosolic complex, so this is correct, though less specific than the cytosol (GO:0005829) annotation also present. Reason: Correct, if general, subcellular localization. Consistent with the more specific cytosol annotation from Reactome. Supporting Evidence: Reactome:R-HSA-71541 The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the subunits of the glycogen phosphorylase (PYGM) dimer. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Subcellular-location keyword mapping to plasma membrane, derived from a possible C-terminal farnesylation (lipid anchor) of the final cysteine. UniProt itself flags the cell-membrane assignment as inferred (ECO:0000305) and notes the terminal tripeptide is probably not removed and the C-terminus is not methylated, casting doubt on a canonical prenylation-driven membrane anchoring. PhK is functionally and structurally characterized as a cytosolic complex. Reason: Plasma membrane localization rests on a weakly supported lipid-anchor inference and is inconsistent with the well-established cytosolic localization of the phosphorylase kinase complex. It is not wrong enough to firmly contradict, but it over-states the evidence and is better treated as a peripheral/uncertain localization rather than a core one. Supporting Evidence: file:human/PHKA1/PHKA1-uniprot.txt Although the final Cys may be farnesylated, the terminal CC tripeptide is probably not removed, and the C-terminus is not CC methylated. Reactome:R-HSA-71541 The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the subunits of the glycogen phosphorylase (PYGM) dimer. |
| GO:0005975 carbohydrate metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO annotation to the very broad "carbohydrate metabolic process" based on the 6-hairpin glycosidase-like superfamily signature of the alpha subunit. PHKA1's actual biological process is much more specific: as part of PhK it drives glycogen breakdown. Reason: The term is correct but far too general. The specific process is glycogen catabolism (glycogenolysis) via activation of glycogen phosphorylase. Replace with the more informative glycogen catabolic process term. Proposed replacements: glycogen catabolic process Supporting Evidence: Reactome:R-HSA-71541 The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the subunits of the glycogen phosphorylase (PYGM) dimer. PMID:33799212 PHKA1 gene codes for the Ξ±M subunit of the PhK, a multimeric protein complex responsible for the control of glycogen breakdown in muscle. |
| GO:0005977 glycogen metabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated (IEA) annotation to glycogen metabolic process. This correctly captures PHKA1's role in glycogen metabolism as a subunit of phosphorylase kinase. Reason: Correct broad biological-process annotation, consistent with UniProt's pathway annotation (glycogen metabolism) and the role of PhK in glycogenolysis. Supporting Evidence: file:human/PHKA1/PHKA1-uniprot.txt Glycan biosynthesis; glycogen metabolism. PMID:33799212 PHKA1 gene codes for the Ξ±M subunit of the PhK, a multimeric protein complex responsible for the control of glycogen breakdown in muscle. |
| GO:0005964 phosphorylase kinase complex | IPI PMID:38548794 Architecture and activation of human muscle phosphorylase ki... | ACCEPT | Summary: Experimental (IPI, ComplexPortal) annotation of PHKA1 as part of the phosphorylase kinase complex, based on the cryo-EM structure of human muscle PhK. Directly confirms the alpha subunit as a structural component bridging the beta subunit and the gamma-delta catalytic subcomplex. Reason: Core, experimentally established annotation. The alpha subunit is an integral part of the PhK holoenzyme. Supporting Evidence: PMID:38548794 The Ξ±-subunit serves as a bridge between the Ξ²-subunit and the Ξ³Ξ΄ subcomplex, and facilitates the Ξ³-subunit to adopt an autoinhibited state. |
| GO:0005980 glycogen catabolic process | IDA PMID:38548794 Architecture and activation of human muscle phosphorylase ki... | ACCEPT | Summary: Experimental (IDA, ComplexPortal) annotation to glycogen catabolic process, from the structural/functional study of human muscle PhK. As the regulatory alpha subunit of the complex that activates glycogen phosphorylase, PHKA1 is directly involved in glycogen catabolism. Reason: This is the core biological process of PHKA1: it is part of the enzyme complex that triggers glycogenolysis by phosphorylating glycogen phosphorylase. Supporting Evidence: Reactome:R-HSA-71541 The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the subunits of the glycogen phosphorylase (PYGM) dimer. PMID:33799212 PHKA1 gene codes for the Ξ±M subunit of the PhK, a multimeric protein complex responsible for the control of glycogen breakdown in muscle. |
| GO:0045819 positive regulation of glycogen catabolic process | IMP PMID:33799212 A novel PHKA1 mutation associating myopathy and cognitive im... | ACCEPT | Summary: Experimental (IMP) annotation to positive regulation of glycogen catabolic process, supported by PHKA1 loss-of-function myopathy: mutations impair muscle PhK activity and glycogen breakdown. As a regulatory subunit whose function (with PKA phosphorylation and Ca2+/calmodulin) is to activate the catalytic gamma subunit, PHKA1 positively regulates glycogenolysis. Reason: Captures the regulatory nature of the alpha subunit well: it is required for and positively contributes to activation of glycogen catabolism, and its loss causes GSD9D muscle phosphorylase kinase deficiency. Supporting Evidence: PMID:33799212 Muscle phosphorylase kinase b deficiency (PhK) is a rare disorder of glycogen metabolism characterized by exercise-induced myalgia and cramps, myoglobinuria and progressive muscle weakness. file:human/PHKA1/PHKA1-uniprot.txt By phosphorylation of various serine residues. CC Allosteric regulation by calcium. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-71541 | ACCEPT | Summary: Traceable author statement (Reactome) localizing PHKA1 to the cytosol as part of the cytosolic phosphorylase kinase complex. Reason: Correct and specific subcellular localization; the phosphorylase kinase complex is cytosolic. Supporting Evidence: Reactome:R-HSA-71541 The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the subunits of the glycogen phosphorylase (PYGM) dimer. |
| GO:0004689 phosphorylase kinase activity | TAS PMID:8226841 The multiphosphorylation domain of the phosphorylase kinase ... | MARK AS OVER ANNOTATED | Summary: Traceable author statement (ProtInc) annotating PHKA1 with phosphorylase kinase activity, citing the cDNA cloning/mRNA-processing study of the alpha M subunit. That paper describes the alpha subunit's multiphosphorylation domain and PKA phosphorylation site; it does not establish that the alpha subunit is itself the catalytic kinase. Phosphorylase kinase activity resides in the intact holoenzyme, with the gamma subunit as catalyst; PHKA1 is a non-catalytic regulatory subunit. Reason: Assigning "enables phosphorylase kinase activity" to the alpha regulatory subunit over-attributes the holoenzyme's catalytic activity. The alpha subunit contributes to (but does not independently enable) this activity; this is represented in core_functions via contributes_to_molecular_function. Supporting Evidence: PMID:8226841 lacks a major part of its multiphosphorylation domain, including the main phosphorylation site for cAMP-dependent protein kinase (PKA) PMID:38548794 The Ξ±- and Ξ²-subunits possess glucoamylase-like domains, but exhibit no detectable enzyme activities. |
| GO:0005977 glycogen metabolic process | TAS PMID:7874115 Human muscle glycogenosis due to phosphorylase kinase defici... | ACCEPT | Summary: Traceable author statement (ProtInc) annotating PHKA1 to glycogen metabolic process, from the first description of a human muscle PhK deficiency caused by a nonsense mutation in the alpha M subunit. Correctly places PHKA1 in glycogen metabolism. Reason: Correct biological-process annotation; PHKA1 is a subunit of the enzyme controlling muscle glycogen breakdown, and its loss causes a glycogen storage disease. Supporting Evidence: PMID:7874115 we identified a nonsense mutation in alpha M. The condition of this patient therefore is a human homolog of the X-linked muscle Phk deficiency |
| GO:0006091 generation of precursor metabolites and energy | TAS PMID:7874115 Human muscle glycogenosis due to phosphorylase kinase defici... | KEEP AS NON CORE | Summary: Traceable author statement (ProtInc) to the broad "generation of precursor metabolites and energy" term. This reflects the downstream physiological consequence of muscle glycogenolysis (mobilizing glucose-1-phosphate to fuel glycolytic ATP during contraction), but it is a very high-level process term not specific to PHKA1's role. Reason: Defensible but non-core: PHKA1's direct role is regulatory activation of glycogenolysis; energy generation is a downstream, general consequence. Retained as a non-core process annotation rather than a defining function. Supporting Evidence: PMID:7874115 we identified a nonsense mutation in alpha M. The condition of this patient therefore is a human homolog of the X-linked muscle Phk deficiency |
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)