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TitleCharacterizing ATP processing by the AAA+ protein p97 at the atomic level.
Journal, issue, pagesNat Chem, Vol. 16, Issue 3, Page 363-372, Year 2024
Publish dateFeb 7, 2024
AuthorsMikhail Shein / Manuel Hitzenberger / Tat Cheung Cheng / Smruti R Rout / Kira D Leitl / Yusuke Sato / Martin Zacharias / Eri Sakata / Anne K Schütz /
PubMed AbstractThe human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an ...The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·P state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.
External linksNat Chem / PubMed:38326645 / PubMed Central
MethodsEM (single particle)
Resolution2.61 - 3.3 Å
Structure data

EMDB-16781: NTD focused cryo-EM map of p97/VCP in ADP.Pi state
Method: EM (single particle) / Resolution: 3.3 Å

17016

8ooi

EMDB-17016, PDB-8ooi:
Full composite cryo-EM map of p97/VCP in ADP.Pi state
Method: EM (single particle) / Resolution: 2.61 Å

EMDB-17024: D1-D2 ring focused cryo-EM map of p97/VCP in ADP.Pi state
Method: EM (single particle) / Resolution: 2.61 Å

EMDB-17128: Consensus cryo-EM map of p97/VCP in ADP.Pi state
Method: EM (single particle) / Resolution: 3.05 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
KeywordsHYDROLASE / AAA+ ATPase / complex

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