5EZV

X-ray crystal structure of AMP-activated protein kinase alpha-2/alpha-1 RIM chimaera (alpha-2(1-347)/alpha-1(349-401)/alpha-2(397-end) beta-1 gamma-1) co-crystallized with C2 (5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • DOI: 10.1038/ncomms10912
  • Primary Citation of Related Structures:  

  • 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 d ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
A, C
560Homo sapiensMutation(s): 0 
Gene Names: PRKAA2 (AMPK, AMPK2), PRKAA1 (AMPK1)
EC: 2.7.11.1 2.7.11.1
Find proteins for P54646 (Homo sapiens)
Go to Gene View: PRKAA2
Go to UniProtKB:  P54646
Find proteins for Q13131 (Homo sapiens)
Go to Gene View: PRKAA1
Go to UniProtKB:  Q13131
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-1
B, D
270Homo sapiensMutation(s): 0 
Gene Names: PRKAB1 (AMPK)
Find proteins for Q9Y478 (Homo sapiens)
Go to Gene View: PRKAB1
Go to UniProtKB:  Q9Y478
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit gamma-1
E, F
336Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
Find proteins for P54619 (Homo sapiens)
Go to Gene View: PRKAG1
Go to UniProtKB:  P54619
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C1V
Query on C1V
Download SDF File 
Download CCD File 
A, 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
 Ligand Interaction
C2Z
Query on C2Z
Download SDF File 
Download CCD File 
E, F
5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid
[5-(5-hydroxy-1,2-oxazol-3-yl)furan-2-yl]phosphonic acid
C7 H6 N O6 P
BRLJHMCTDKAUAY-UHFFFAOYSA-N
 Ligand Interaction
STU
Query on STU
Download SDF File 
Download CCD File 
A, C
STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C1VKd: 487 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.608α = 90.00
b = 134.112β = 93.16
c = 141.287γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references