4MUV

M. loti cyclic-nucleotide binding domain mutant displaying inverted ligand selectivity, cyclic-GMP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel.

Pessoa, J.Fonseca, F.Furini, S.Morais-Cabral, J.H.

(2014) J.Gen.Physiol. 144: 41-54

  • DOI: 10.1085/jgp.201311145

  • PubMed Abstract: 
  • Cyclic nucleotide-binding (CNB) domains regulate the activity of channels, kinases, exchange factors, and transcription factors. These proteins are highly variable in their ligand selectivity; some are highly selective for either cAMP or cGMP, wherea ...

    Cyclic nucleotide-binding (CNB) domains regulate the activity of channels, kinases, exchange factors, and transcription factors. These proteins are highly variable in their ligand selectivity; some are highly selective for either cAMP or cGMP, whereas others are not. Several molecular determinants of ligand selectivity in CNB domains have been defined, but these do not provide a complete view of the selectivity mechanism. We performed a thorough analysis of the ligand-binding properties of mutants of the CNB domain from the MlotiK1 potassium channel. In particular, we defined which residues specifically favor cGMP or cAMP. Inversion of ligand selectivity, from favoring cAMP to favoring cGMP, was only achieved through a combination of three mutations in the ligand-binding pocket. We determined the x-ray structure of the triple mutant bound to cGMP and performed molecular dynamics simulations and a biochemical analysis of the effect of the mutations. We concluded that the increase in cGMP affinity and selectivity does not result simply from direct interactions between the nucleotide base and the amino acids introduced in the ligand-binding pocket residues. Rather, tighter cGMP binding over cAMP results from the polar chemical character of the mutations, from greater accessibility of water molecules to the ligand in the bound state, and from an increase in the structural flexibility of the mutated binding pocket.


    Organizational Affiliation

    Instituto de Biologia Molecular e Celular and Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4150-180 Porto, PortugalInstituto de Biologia Molecular e Celular and Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4150-180 Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclic nucleotide-gated potassium channel mll3241
A, B
142Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)Mutation(s): 3 
Find proteins for Q98GN8 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Go to UniProtKB:  Q98GN8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PCG
Query on PCG

Download SDF File 
Download CCD File 
A, B
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PCGKd: 336 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.051α = 90.00
b = 61.572β = 90.00
c = 67.844γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
EDNAdata collection
XSCALEdata scaling
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references