5BV6

PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with cGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II.

Campbell, J.C.Kim, J.J.Li, K.Y.Huang, G.Y.Reger, A.S.Matsuda, S.Sankaran, B.Link, T.M.Yuasa, K.Ladbury, J.E.Casteel, D.E.Kim, C.

(2016) J.Biol.Chem. 291: 5623-5633

  • DOI: 10.1074/jbc.M115.691303
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Membrane-bound cGMP-dependent protein kinase (PKG) II is a key regulator of bone growth, renin secretion, and memory formation. Despite its crucial physiological roles, little is known about its cyclic nucleotide selectivity mechanism due to a lack o ...

    Membrane-bound cGMP-dependent protein kinase (PKG) II is a key regulator of bone growth, renin secretion, and memory formation. Despite its crucial physiological roles, little is known about its cyclic nucleotide selectivity mechanism due to a lack of structural information. Here, we find that the C-terminal cyclic nucleotide binding (CNB-B) domain of PKG II binds cGMP with higher affinity and selectivity when compared with its N-terminal CNB (CNB-A) domain. To understand the structural basis of cGMP selectivity, we solved co-crystal structures of the CNB domains with cyclic nucleotides. Our structures combined with mutagenesis demonstrate that the guanine-specific contacts at Asp-412 and Arg-415 of the αC-helix of CNB-B are crucial for cGMP selectivity and activation of PKG II. Structural comparison with the cGMP selective CNB domains of human PKG I and Plasmodium falciparum PKG (PfPKG) shows different contacts with the guanine moiety, revealing a unique cGMP selectivity mechanism for PKG II.


    Organizational Affiliation

    From the Structural and Computational Biology and Molecular Biophysics Program.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent protein kinase 2
A
152Homo sapiensGene Names: PRKG2 (PRKGR2)
EC: 2.7.11.12
Find proteins for Q13237 (Homo sapiens)
Go to Gene View: PRKG2
Go to UniProtKB:  Q13237
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
35G
Query on 35G

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A
GUANOSINE-3',5'-MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.344α = 90.00
b = 50.479β = 90.00
c = 69.167γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
iMOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM090161

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2016-03-02
    Type: Structure summary
  • Version 1.3: 2016-03-23
    Type: Database references
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.5: 2017-10-11
    Type: Refinement description