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TitleDynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 917, Year 2025
Publish dateJan 22, 2025
AuthorsChen Wang / Cheng Ma / Yuanyou Xu / Shenghai Chang / Hangjun Wu / Chunlan Yan / Jinghua Chen / Yongping Wu / Shaoya An / Jiaqi Xu / Qin Han / Yujie Jiang / Zhinong Jiang / Xiakun Chu / Haichun Gao / Xing Zhang / Yunjie Chang /
PubMed AbstractThe multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all ...The multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all components have been individually characterized, the intact PDHc structure remains unclear, hampering our understanding of its composition and dynamical catalytic mechanisms. Here, we report the in-situ architecture of intact mammalian PDHc by cryo-electron tomography. The organization of peripheral E1 and E3 components varies substantially among the observed PDHcs, with an average of 21 E1 surrounding each PDHc core, and up to 12 E3 locating primarily along the pentagonal openings. In addition, we observed dynamic interactions of the substrate translocating lipoyl domains (LDs) with both E1 and E2, and the interaction interfaces were further analyzed by molecular dynamics simulations. By revealing intrinsic dynamics of PDHc peripheral compositions, our findings indicate a distinctive activity regulation mechanism, through which the number of E1, E3 and functional LDs may be coordinated to meet constantly changing demands of metabolism.
External linksNat Commun / PubMed:39843418 / PubMed Central
MethodsEM (subtomogram averaging) / EM (single particle)
Resolution3.2 - 15.0 Å
Structure data

EMDB-38712: The structure of the core of the pyruvate dehydrogenase complex in the mitochondria of pig hearts.
Method: EM (subtomogram averaging) / Resolution: 4.3 Å

EMDB-38716: The conformation of E3 with PSBD in E2 components of pyruvate dehydrogenase complex
Method: EM (subtomogram averaging) / Resolution: 15.0 Å

61080

9j1w

EMDB-61080, PDB-9j1w:
Endogenous dihydrolipoamide acetyltransferase (E2) core of pyruvate dehydrogenase complex from pig heart
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-61081: The map of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2
Method: EM (subtomogram averaging) / Resolution: 8.7 Å

EMDB-61082: The map of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain and lipoyl domain of E2
Method: EM (subtomogram averaging) / Resolution: 8.2 Å

EMDB-61083: The trimer of the pyruvate dehydrogenase complex core
Method: EM (subtomogram averaging) / Resolution: 6.2 Å

EMDB-61084: The conformation of lipoy domain binding the core of the pyruvate dehydrogenase complex.
Method: EM (subtomogram averaging) / Resolution: 6.9 Å

Source
  • sus scrofa (pig)
KeywordsTRANSFERASE / pyruvate dehydrogenase complex / dihydrolipoamide acetyltransferase / endogenous / STRUCTURAL PROTEIN

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