4ZHX

Novel binding site for allosteric activation of AMPK

• PDB DOI: https://doi.org/10.2210/pdb4ZHX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-04-27 Released: 2016-03-09 
• Deposition Author(s): Langendorf, C.G., Ngoei, K.R., Issa, S.M.A., Ling, N., Gorman, M.A., Parker, M.W., Sakamoto, K., Scott, J.W., Oakhill, J.S., Kemp, B.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.243 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 

Starting Model: experimental

Literature

Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding.

Langendorf, C.G., Ngoei, K.R., Scott, J.W., Ling, N.X., Issa, S.M., Gorman, M.A., Parker, M.W., Sakamoto, K., Oakhill, J.S., Kemp, B.E.

(2016) Nat Commun 7: 10912-10912

• PubMed: 26952388 
• DOI: https://doi.org/10.1038/ncomms10912
• Primary Citation of Related Structures:  
  4ZHX, 5EZV


• PubMed Abstract: 
  

  The metabolic stress-sensing enzyme AMP-activated protein kinase (AMPK) is responsible for regulating metabolism in response to energy supply and demand. Drugs that activate AMPK may be useful in the treatment of metabolic diseases including type 2 diabetes. We have determined the crystal structure of AMPK in complex with its activator 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid (C2), revealing two C2-binding sites in the γ-subunit distinct from nucleotide sites. C2 acts synergistically with the drug A769662 to activate AMPK α1-containing complexes independent of upstream kinases. Our results show that dual drug therapies could be effective AMPK-targeting strategies to treat metabolic diseases.

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Organizational Affiliation: 

Protein Chemistry &Metabolism, St Vincent's Institute of Medical Research, University of Melbourne, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 268.12 kDa 
• Atom Count: 14,587 
• Modelled Residue Count: 1,807 
• Deposited Residue Count: 2,342 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-2	A, C	565	Homo sapiens	Mutation(s): 1  Gene Names: PRKAA2, AMPK, AMPK2 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P54646 (Homo sapiens) Explore P54646  Go to UniProtKB:  P54646
PHAROS:  P54646 GTEx:  ENSG00000162409

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-1	B, D	270	Homo sapiens	Mutation(s): 0  Gene Names: PRKAB1, AMPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y478 (Homo sapiens) Explore Q9Y478  Go to UniProtKB:  Q9Y478
PHAROS:  Q9Y478 GTEx:  ENSG00000111725

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit gamma-1	E, F	336	Homo sapiens	Mutation(s): 0  Gene Names: PRKAG1
UniProt & NIH Common Fund Data Resources
Find proteins for P54619 (Homo sapiens) Explore P54619  Go to UniProtKB:  P54619
PHAROS:  P54619 GTEx:  ENSG00000181929

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4O7	G [auth A], I [auth C]	(5S,6R,7R,9R,13cR,14R,16aS)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16a-octahydro-5H,13cH-5,9-epoxy-4b,9a,1 5-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-ol C28 H30 N4 O3 FJJCTPAMIAOFJX-VWKRKTLRSA-N
C1V	H [auth B], J [auth C]	3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile C20 H12 N2 O3 S CTESJDQKVOEUOY-UHFFFAOYSA-N
AMP	M [auth F], N [auth F]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
C2Z	K [auth E], L [auth E]	5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid C7 H6 N O6 P BRLJHMCTDKAUAY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, C	L-PEPTIDE LINKING	C4 H10 N O6 P		THR
SEP	B, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
C1V	BindingDB:  4ZHX	Kd: min: 487, max: 1.45e+4 (nM) from 3 assay(s)
		EC50: min: 390, max: 800 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.243 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.95	α = 90
b = 134.24	β = 93.02
c = 141.48	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Langendorf, C.G., Ngoei, K.R., Issa, S.M.A., Ling, N., Gorman, M.A., Parker, M.W., Sakamoto, K., Scott, J.W., Oakhill, J.S., Kemp, B.E.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.4: 2024-11-20
  Changes: Structure summary