2QRE

Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide (ZMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

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This is version 1.2 of the entry. See complete history


Literature

Structural Insight into AMPK Regulation: ADP Comes into Play.

Jin, X.Townley, R.Shapiro, L.

(2007) Structure 15: 1285-1295

  • DOI: https://doi.org/10.1016/j.str.2007.07.017
  • Primary Citation of Related Structures:  
    2QR1, 2QRC, 2QRD, 2QRE

  • PubMed Abstract: 

    The AMP-activated protein kinase (AMPK), a sensor of cellular energy status found in all eukaryotes, responds to changes in intracellular adenosine nucleotide levels resulting from metabolic stresses. Here we describe crystal structures of a heterotrimeric regulatory core fragment from Schizosaccharomyces pombe AMPK in complex with ADP, ADP/AMP, ADP/ATP, and 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide (AICAR phosphate, or ZMP), a well-characterized AMPK activator. Prior crystallographic studies had revealed a single site in the gamma subunit that binds either ATP or AMP within Bateman domain B. Here we show that ZMP binds at this site, mimicking the binding of AMP. An analogous site in Bateman domain A selectively accommodates ADP, which binds in a distinct manner that also involves direct ligation to elements from the beta subunit. These observations suggest a possible role for ADP in regulating AMPK response to changes in cellular energy status.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SNF1-like protein kinase ssp2A,
D [auth C]
137Schizosaccharomyces pombeMutation(s): 0 
Gene Names: ssp2
EC: 2.7.11.1
UniProt
Find proteins for O74536 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74536 
Go to UniProtKB:  O74536
Entity Groups  
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UniProt GroupO74536
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SPCC1919.03c proteinB,
E [auth D]
97Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P78789 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P78789 
Go to UniProtKB:  P78789
Entity Groups  
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UniProt GroupP78789
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein C1556.08cC [auth G],
F [auth E]
334Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10343 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q10343 
Go to UniProtKB:  Q10343
Entity Groups  
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UniProt GroupQ10343
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMZ
Query on AMZ

Download Ideal Coordinates CCD File 
G,
H [auth E]
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
C9 H15 N4 O8 P
NOTGFIUVDGNKRI-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.47α = 90
b = 78.146β = 124.04
c = 108.512γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations