4QX5

Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: Insights for PKG agonist design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.318 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


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Literature

Neutron Diffraction Reveals Hydrogen Bonds Critical for cGMP-Selective Activation: Insights for cGMP-Dependent Protein Kinase Agonist Design.

Huang, G.Y.Gerlits, O.O.Blakeley, M.P.Sankaran, B.Kovalevsky, A.Y.Kim, C.

(2014) Biochemistry 53: 6725-6727

  • DOI: 10.1021/bi501012v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High selectivity of cyclic-nucleotide binding (CNB) domains for cAMP and cGMP are required for segregating signaling pathways; however, the mechanism of selectivity remains unclear. To investigate the mechanism of high selectivity in cGMP-dependent p ...

    High selectivity of cyclic-nucleotide binding (CNB) domains for cAMP and cGMP are required for segregating signaling pathways; however, the mechanism of selectivity remains unclear. To investigate the mechanism of high selectivity in cGMP-dependent protein kinase (PKG), we determined a room-temperature joint X-ray/neutron (XN) structure of PKG Iβ CNB-B, a domain 200-fold selective for cGMP over cAMP, bound to cGMP (2.2 Å), and a low-temperature X-ray structure of CNB-B with cAMP (1.3 Å). The XN structure directly describes the hydrogen bonding interactions that modulate high selectivity for cGMP, while the structure with cAMP reveals that all these contacts are disrupted, explaining its low affinity for cAMP.


    Organizational Affiliation

    Verna and Mars McClean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, Texas 77004, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent protein kinase 1
A
153Homo sapiensMutation(s): 0 
Gene Names: PRKG1 (PRKG1B, PRKGR1A, PRKGR1B)
EC: 2.7.11.12
Find proteins for Q13976 (Homo sapiens)
Go to Gene View: PRKG1
Go to UniProtKB:  Q13976
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CMP
Query on CMP

Download SDF File 
Download CCD File 
A
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
CYCLIC AMP; CAMP
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.318 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 48.440α = 90.00
b = 48.440β = 90.00
c = 103.462γ = 90.00
Software Package:
Software NamePurpose
Specdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description