6C9G

AMP-activated protein kinase bound to pharmacological activator R739

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

  • Deposited: 2018-01-26 Released: 2018-11-28 
  • Deposition Author(s): Yan, Y., Zhou, X.E., Novick, S., Shaw, S.J., Li, Y., Hitoshi, Y., Brunzelle, J.S., Griffin, P.R., Xu, H.E., Melcher, K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China), Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.

Yan, Y., Zhou, X.E., Novick, S.J., Shaw, S.J., Li, Y., Brunzelle, J.S., Hitoshi, Y., Griffin, P.R., Xu, H.E., Melcher, K.

(2019) J Biol Chem 294: 953-967

  • DOI: 10.1074/jbc.RA118.004883
  • Primary Citation of Related Structures:  
    6C9F, 6C9G, 6C9H, 6C9J

  • PubMed Abstract: 

    • AMP-activated protein kinase (AMPK) is an attractive therapeutic target for managing metabolic diseases. A class of pharmacological activators, including Merck 991, binds the AMPK ADaM site, which forms the interaction surface between the kinase domain (KD) of the α-subunit and the carbohydrate-binding module (CBM) of the β-subunit ...

    AMP-activated protein kinase (AMPK) is an attractive therapeutic target for managing metabolic diseases. A class of pharmacological activators, including Merck 991, binds the AMPK ADaM site, which forms the interaction surface between the kinase domain (KD) of the α-subunit and the carbohydrate-binding module (CBM) of the β-subunit. Here, we report the development of two new 991-derivative compounds, R734 and R739, which potently activate AMPK in a variety of cell types, including β 2 -specific skeletal muscle cells. Surprisingly, we found that they have only minor effects on direct kinase activity of the recombinant α 1 β 2 γ 1 isoform yet robustly enhance protection against activation loop dephosphorylation. This mode of activation is reminiscent of that of ADP, which activates AMPK by binding to the nucleotide-binding sites in the γ-subunit, more than 60 Å away from the ADaM site. To understand the mechanisms of full and partial AMPK activation, we determined the crystal structures of fully active phosphorylated AMPK α 1 β 1 γ 1 bound to AMP and R734/R739 as well as partially active nonphosphorylated AMPK bound to R734 and AMP and phosphorylated AMPK bound to R734 in the absence of added nucleotides at <3-Å resolution. These structures and associated analyses identified a novel conformational state of the AMPK autoinhibitory domain associated with partial kinase activity and provide new insights into phosphorylation-dependent activation loop stabilization in AMPK.

    Organizational Affiliation: 

    From the Center of Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503, karsten.melcher@vai.org.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-1,5'-AMP-activated protein kinase catalytic subunit alpha-1A494Homo sapiensMutation(s): 0 
Gene Names: PRKAA1, AMPK1
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13131 (Homo sapiens)
Explore Q13131 
Go to UniProtKB:  Q13131
PHAROS:  Q13131
Entity Groups  
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UniProt GroupQ13131
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit beta-1B204Homo sapiensMutation(s): 1 
Gene Names: PRKAB1, AMPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y478 (Homo sapiens)
Explore Q9Y478 
Go to UniProtKB:  Q9Y478
PHAROS:  Q9Y478
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UniProt GroupQ9Y478
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit gamma-1C331Homo sapiensMutation(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
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UniProt GroupP54619
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R93
Query on R93
Download Ideal Coordinates CCD File 
D [auth A]5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide
C27 H20 Cl N3 O4
YSNIPFQCRHRGSO-UHFFFAOYSA-N		 Ligand Interaction
STU
Query on STU
Download Ideal Coordinates CCD File 
E [auth A]STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N		 Ligand Interaction
AMP
Query on AMP
Download Ideal Coordinates CCD File 
F [auth C],
G [auth C],
H [auth C]		ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.986α = 90
b = 122.986β = 90
c = 406.048γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102545
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK071662
National Natural Science Foundation of China (NSFC)China31300245
Ministry of Science and Technology (MoST, China)China2012ZX09301001
Ministry of Science and Technology (MoST, China)China2012CB910403
Ministry of Science and Technology (MoST, China)China2013CB910600
Ministry of Science and Technology (MoST, China)ChinaXDB08020303
Ministry of Science and Technology (MoST, China)China2013ZX09507001
Michigan Economic Development Corporation and the Michigan Technology Tri-CorridorUnited States085P1000817

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence, Database references