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Structure paper

TitleStructure of an AMPK complex in an inactive, ATP-bound state.
Journal, issue, pagesScience, Vol. 373, Issue 6553, Page 413-419, Year 2021
Publish dateJul 23, 2021
AuthorsYan Yan / Somnath Mukherjee / Kaleeckal G Harikumar / Timothy S Strutzenberg / X Edward Zhou / Kelly Suino-Powell / Ting-Hai Xu / Ryan D Sheldon / Jared Lamp / Joseph S Brunzelle / Katarzyna Radziwon / Abigail Ellis / Scott J Novick / Irving E Vega / Russell G Jones / Laurence J Miller / H Eric Xu / Patrick R Griffin / Anthony A Kossiakoff / Karsten Melcher /
PubMed AbstractAdenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in ...Adenosine monophosphate (AMP)-activated protein kinase (AMPK) regulates metabolism in response to the cellular energy states. Under energy stress, AMP stabilizes the active AMPK conformation, in which the kinase activation loop (AL) is protected from protein phosphatases, thus keeping the AL in its active, phosphorylated state. At low AMP:ATP (adenosine triphosphate) ratios, ATP inhibits AMPK by increasing AL dynamics and accessibility. We developed conformation-specific antibodies to trap ATP-bound AMPK in a fully inactive, dynamic state and determined its structure at 3.5-angstrom resolution using cryo-electron microscopy. A 180° rotation and 100-angstrom displacement of the kinase domain fully exposes the AL. On the basis of the structure and supporting biophysical data, we propose a multistep mechanism explaining how adenine nucleotides and pharmacological agonists modulate AMPK activity by altering AL phosphorylation and accessibility.
External linksScience / PubMed:34437114 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.47 - 5.5 Å
Structure data

22336

7jhg

EMDB-22336, PDB-7jhg:
Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody
Method: EM (single particle) / Resolution: 3.47 Å

22337

7jhh

EMDB-22337, PDB-7jhh:
Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody
Method: EM (single particle) / Resolution: 3.92 Å

23708

7m74

EMDB-23708, PDB-7m74:
ATP-bound AMP-activated protein kinase
Method: EM (single particle) / Resolution: 3.93 Å

PDB-7jij:
ATP-bound AMP-activated protein kinase
Method: X-RAY DIFFRACTION / Resolution: 5.5 Å

Chemicals

ChemComp-TAK:
6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine

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

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

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

Source
  • homo sapiens (human)
  • synthetic construct (others)
  • escherichia coli k-12 (bacteria)
  • escherichia coli (E. coli)
  • lama glama (llama)
KeywordsTRANSFERASE/IMMUNE SYSTEM / AMPK / ATP / fully inactive / KD-displaced / TRANSFERASE-IMMUNE SYSTEM complex / SIGNALING PROTEIN / activation / ATP-binding

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