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TitleMolecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 3020, Year 2025
Publish dateMar 28, 2025
AuthorsRuifang Ma / Bowen Du / Chen Shi / Lei Wang / Fuxing Zeng / Jie Han / Huiyi Guan / Yong Wang / Kaige Yan /
PubMed AbstractPhosphorylase kinase (PhK) regulates the degradation of glycogen by integrating diverse signals, providing energy to the organism. Dysfunctional mutations may directly lead to Glycogen Storage ...Phosphorylase kinase (PhK) regulates the degradation of glycogen by integrating diverse signals, providing energy to the organism. Dysfunctional mutations may directly lead to Glycogen Storage Disease type IX (GSD IX), whereas the abnormal expression of PhK is also associated with tumors. Here, we use cryo-electron microscopy (cryo-EM) to resolve its near-atomic structures in the inactive and active states. These structures reveal the interactions and relative locations of the four subunits (αβγδ) within the PhK complex. Phosphorylated α and β subunits induce PhK to present a more compact state, while Ca causes sliding of the δ subunit along the helix of the γ subunit. Both actions synergistically activate PhK by enabling the de-inhibition of the γ subunit. We also identified different binding modes between PhK and its substrate, glycogen phosphorylase (GP), in two distinct states, using cross-linking mass spectrometry (XL-MS). This study provides valuable insights into the regulatory mechanisms of PhK, thereby enhancing our understanding of GSD IX and its implications in tumorigenesis.
External linksNat Commun / PubMed:40148320 / PubMed Central
MethodsEM (single particle)
Resolution3.23 - 4.24 Å
Structure data

39775

8z5m

EMDB-39775, PDB-8z5m:
human phosphorylase kinase alpha/gamma/delta subcomplex - inactive state
Method: EM (single particle) / Resolution: 3.66 Å

39777

8z5p

EMDB-39777, PDB-8z5p:
human phosphorylase kinase - inactive state
Method: EM (single particle) / Resolution: 3.41 Å

39778

8z5q

EMDB-39778, PDB-8z5q:
human phosphorylase kinase - inactive state
Method: EM (single particle) / Resolution: 4.24 Å

39779

8z5r

EMDB-39779, PDB-8z5r:
human phosphorylase kinase alpha/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
Method: EM (single particle) / Resolution: 3.52 Å

39781

8z5t

EMDB-39781, PDB-8z5t:
human phosphorylase kinase - phosphorylation and Ca2+ bound state
Method: EM (single particle) / Resolution: 3.74 Å

EMDB-39784: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - inactive state
Method: EM (single particle) / Resolution: 3.34 Å

EMDB-39785: human phosphorylase kinase alpha/beta/gamma/delta subcomplex - phosphorylation and Ca2+ bound state
Method: EM (single particle) / Resolution: 3.23 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
KeywordsCYTOSOLIC PROTEIN / Kinase / glycogenolysis / SIGNALING PROTEIN

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