id: P46020
gene_symbol: PHKA1
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  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.
alternative_products:
- name: 1 (AC)
  id: P46020-1
- name: 2 (C)
  id: P46020-2
  sequence_note: VSP_004697
- name: '3'
  id: P46020-3
  sequence_note: VSP_042517, VSP_042518
existing_annotations:
- term:
    id: GO:0005964
    label: phosphorylase kinase complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: part_of
  review:
    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.
    action: ACCEPT
    reason: >-
      Complex membership is a core, correct annotation for PHKA1. The alpha subunit is an
      integral, structurally defined component of the phosphorylase kinase holoenzyme.
    supported_by:
    - reference_id: PMID:38548794
      supporting_text: >-
        The 1.3-megadalton PhK α4β4γ4δ4 hexadecamer consists of a tetramer of tetramer,
        wherein four αβγδ modules are connected by the central β4 scaffold.
    - reference_id: file:human/PHKA1/PHKA1-uniprot.txt
      supporting_text: >-
        Alpha (PHKA1 or PHKA2) and beta (PHKB)
        CC       are regulatory subunits, gamma (PHKG1 or PHKG2) is the catalytic
        CC       subunit, and delta is calmodulin.
- term:
    id: GO:0004689
    label: phosphorylase kinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:38548794
      supporting_text: >-
        The α- and β-subunits possess glucoamylase-like domains, but exhibit no detectable
        enzyme activities.
    - reference_id: file:human/PHKA1/PHKA1-uniprot.txt
      supporting_text: >-
        Alpha (PHKA1 or PHKA2) and beta (PHKB)
        CC       are regulatory subunits, gamma (PHKG1 or PHKG2) is the catalytic
        CC       subunit, and delta is calmodulin.
- term:
    id: GO:0005516
    label: calmodulin binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:human/PHKA1/PHKA1-uniprot.txt
      supporting_text: >-
        Phosphorylase b kinase catalyzes the phosphorylation of
        CC       serine in certain substrates, including troponin I. The alpha chain may
        CC       bind calmodulin.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  review:
    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.
    action: ACCEPT
    reason: >-
      Correct, if general, subcellular localization. Consistent with the more specific
      cytosol annotation from Reactome.
    supported_by:
    - reference_id: Reactome:R-HSA-71541
      supporting_text: >-
        The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the
        subunits of the glycogen phosphorylase (PYGM) dimer.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: file:human/PHKA1/PHKA1-uniprot.txt
      supporting_text: >-
        Although the final Cys may be farnesylated, the terminal
        CC       tripeptide is probably not removed, and the C-terminus is not
        CC       methylated.
    - reference_id: Reactome:R-HSA-71541
      supporting_text: >-
        The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the
        subunits of the glycogen phosphorylase (PYGM) dimer.
- term:
    id: GO:0005975
    label: carbohydrate metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0005980
      label: glycogen catabolic process
    supported_by:
    - reference_id: Reactome:R-HSA-71541
      supporting_text: >-
        The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the
        subunits of the glycogen phosphorylase (PYGM) dimer.
    - reference_id: PMID:33799212
      supporting_text: >-
        PHKA1 gene codes for the αM subunit of the PhK, a multimeric protein complex
        responsible for the control of glycogen breakdown in muscle.
- term:
    id: GO:0005977
    label: glycogen metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      Combined automated (IEA) annotation to glycogen metabolic process. This correctly
      captures PHKA1's role in glycogen metabolism as a subunit of phosphorylase kinase.
    action: ACCEPT
    reason: >-
      Correct broad biological-process annotation, consistent with UniProt's pathway
      annotation (glycogen metabolism) and the role of PhK in glycogenolysis.
    supported_by:
    - reference_id: file:human/PHKA1/PHKA1-uniprot.txt
      supporting_text: "Glycan biosynthesis; glycogen metabolism."
    - reference_id: PMID:33799212
      supporting_text: >-
        PHKA1 gene codes for the αM subunit of the PhK, a multimeric protein complex
        responsible for the control of glycogen breakdown in muscle.
- term:
    id: GO:0005964
    label: phosphorylase kinase complex
  evidence_type: IPI
  original_reference_id: PMID:38548794
  qualifier: part_of
  review:
    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.
    action: ACCEPT
    reason: >-
      Core, experimentally established annotation. The alpha subunit is an integral part of
      the PhK holoenzyme.
    supported_by:
    - reference_id: PMID:38548794
      supporting_text: >-
        The α-subunit serves as a bridge between the β-subunit and the γδ subcomplex, and
        facilitates the γ-subunit to adopt an autoinhibited state.
- term:
    id: GO:0005980
    label: glycogen catabolic process
  evidence_type: IDA
  original_reference_id: PMID:38548794
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    reason: >-
      This is the core biological process of PHKA1: it is part of the enzyme complex that
      triggers glycogenolysis by phosphorylating glycogen phosphorylase.
    supported_by:
    - reference_id: Reactome:R-HSA-71541
      supporting_text: >-
        The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the
        subunits of the glycogen phosphorylase (PYGM) dimer.
    - reference_id: PMID:33799212
      supporting_text: >-
        PHKA1 gene codes for the αM subunit of the PhK, a multimeric protein complex
        responsible for the control of glycogen breakdown in muscle.
- term:
    id: GO:0045819
    label: positive regulation of glycogen catabolic process
  evidence_type: IMP
  original_reference_id: PMID:33799212
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:33799212
      supporting_text: >-
        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.
    - reference_id: file:human/PHKA1/PHKA1-uniprot.txt
      supporting_text: >-
        By phosphorylation of various serine residues.
        CC       Allosteric regulation by calcium.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-71541
  qualifier: located_in
  review:
    summary: >-
      Traceable author statement (Reactome) localizing PHKA1 to the cytosol as part of the
      cytosolic phosphorylase kinase complex.
    action: ACCEPT
    reason: >-
      Correct and specific subcellular localization; the phosphorylase kinase complex is
      cytosolic.
    supported_by:
    - reference_id: Reactome:R-HSA-71541
      supporting_text: >-
        The cytosolic phosphorylase kinase complex catalyzes the phosphorylation of the
        subunits of the glycogen phosphorylase (PYGM) dimer.
- term:
    id: GO:0004689
    label: phosphorylase kinase activity
  evidence_type: TAS
  original_reference_id: PMID:8226841
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:8226841
      supporting_text: >-
        lacks a major part of its multiphosphorylation domain, including the main
        phosphorylation site for cAMP-dependent protein kinase (PKA)
    - reference_id: PMID:38548794
      supporting_text: >-
        The α- and β-subunits possess glucoamylase-like domains, but exhibit no detectable
        enzyme activities.
- term:
    id: GO:0005977
    label: glycogen metabolic process
  evidence_type: TAS
  original_reference_id: PMID:7874115
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    reason: >-
      Correct biological-process annotation; PHKA1 is a subunit of the enzyme controlling
      muscle glycogen breakdown, and its loss causes a glycogen storage disease.
    supported_by:
    - reference_id: PMID:7874115
      supporting_text: >-
        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
- term:
    id: GO:0006091
    label: generation of precursor metabolites and energy
  evidence_type: TAS
  original_reference_id: PMID:7874115
  qualifier: involved_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:7874115
      supporting_text: >-
        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
core_functions:
- description: >-
    PHKA1 is the muscle alpha regulatory subunit of phosphorylase kinase. It is non-catalytic
    (a glucoamylase-like fold with no detectable enzyme activity) and contributes to the
    complex-level phosphorylase kinase activity by bridging the beta subunit to the
    gamma-delta catalytic subcomplex and holding the catalytic gamma subunit in an
    autoinhibited state until activation by PKA phosphorylation and Ca2+/calmodulin.
  molecular_function:
    id: GO:0005516
    label: calmodulin binding
  contributes_to_molecular_function:
    id: GO:0004689
    label: phosphorylase kinase activity
  directly_involved_in:
  - id: GO:0005980
    label: glycogen catabolic process
  - id: GO:0045819
    label: positive regulation of glycogen catabolic process
  locations:
  - id: GO:0005829
    label: cytosol
  in_complex:
    id: GO:0005964
    label: phosphorylase kinase complex
  supported_by:
  - reference_id: PMID:38548794
    supporting_text: >-
      The α-subunit serves as a bridge between the β-subunit and the γδ subcomplex, and
      facilitates the γ-subunit to adopt an autoinhibited state.
  - reference_id: PMID:38548794
    supporting_text: >-
      The α- and β-subunits possess glucoamylase-like domains, but exhibit no detectable
      enzyme activities.
  - reference_id: file:human/PHKA1/PHKA1-uniprot.txt
    supporting_text: >-
      Alpha (PHKA1 or PHKA2) and beta (PHKB)
      CC       are regulatory subunits, gamma (PHKG1 or PHKG2) is the catalytic
      CC       subunit, and delta is calmodulin.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:33799212
  title: 'A novel PHKA1 mutation associating myopathy and cognitive impairment: Expanding
    the spectrum of phosphorylase kinase b (PhK) deficiency.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified. Abstract explicitly states PHKA1 encodes the alpha M subunit of PhK,
      a multimeric complex controlling muscle glycogen breakdown, and that deficiency causes
      X-linked GSD VIII/IXd. Directly supports PHKA1's role and the disease.
- id: PMID:38548794
  title: Architecture and activation of human muscle phosphorylase kinase.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified. Cryo-EM structure of human muscle PhK establishing that the alpha and
      beta subunits are non-catalytic (glucoamylase-like fold, no detectable activity) and
      that the alpha subunit bridges beta to the gamma-delta subcomplex and maintains gamma
      autoinhibition. Key evidence that PHKA1 is regulatory, not catalytic.
- id: PMID:7874115
  title: Human muscle glycogenosis due to phosphorylase kinase deficiency associated
    with a nonsense mutation in the muscle isoform of the alpha subunit.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified. First human PHKA1 (alpha M) mutation causing X-linked muscle PhK
      deficiency; supports glycogen metabolic process involvement and disease association.
- id: PMID:8226841
  title: The multiphosphorylation domain of the phosphorylase kinase alpha M and alpha
    L subunits is a hotspot of differential mRNA processing and of molecular evolution.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified. Cloning/sequencing of the human alpha M subunit and characterization
      of its multiphosphorylation (PKA) domain and splicing. Supports the regulatory
      phosphorylation biology; does not establish PHKA1 as catalytic, so the TAS
      phosphorylase kinase activity annotation it underlies is treated as over-annotated.
- id: Reactome:R-HSA-71541
  title: glycogen phosphorylase (PYGM) dimer b + 2 ATP => glycogen phosphorylase (PYGM)
    dimer a + 2 ADP
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Reactome reaction in which the cytosolic phosphorylase kinase complex (including PHKA1)
      phosphorylates glycogen phosphorylase (PYGM) b to a. Supports cytosolic localization and
      the glycogen catabolic role of the complex.
- id: file:human/PHKA1/PHKA1-uniprot.txt
  title: UniProtKB record for human PHKA1 (P46020)
  findings:
  - statement: >-
      UniProt describes PHKA1 as the skeletal-muscle alpha regulatory subunit of
      phosphorylase kinase; alpha and beta are regulatory subunits, gamma is catalytic, and
      delta is calmodulin. The alpha chain may bind calmodulin; the complex is regulated by
      serine phosphorylation and allosterically by calcium.