4JG4

Ligand concentration regulates the pathways of coupled protein folding and binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ligand concentration regulates the pathways of coupled protein folding and binding.

Daniels, K.G.Tonthat, N.K.McClure, D.R.Chang, Y.C.Liu, X.Schumacher, M.A.Fierke, C.A.Schmidler, S.C.Oas, T.G.

(2014) J Am Chem Soc 136: 822-825

  • DOI: 10.1021/ja4086726
  • Primary Citation of Related Structures:  
    4JG4

  • PubMed Abstract: 
  • Coupled ligand binding and conformational change plays a central role in biological regulation. Ligands often regulate protein function by modulating conformational dynamics, yet the order in which binding and conformational change occurs are often h ...

    Coupled ligand binding and conformational change plays a central role in biological regulation. Ligands often regulate protein function by modulating conformational dynamics, yet the order in which binding and conformational change occurs are often hotly debated. Here we show that the "conformational selection versus induced fit" distinction on which this debate is based is a false dichotomy because the mechanism depends on ligand concentration. Using the binding of pyrophosphate (PPi) to Bacillus subtilis RNase P protein as a model, we show that coupled reactions are best understood as a change in flux between competing pathways with distinct orders of binding and conformational change. The degree of partitioning through each pathway depends strongly on PPi concentration, with ligand binding redistributing the conformational ensemble toward the folded state by both increasing folding rates and decreasing unfolding rates. These results indicate that ligand binding induces marked and varied changes in protein conformational dynamics, and that the order of binding and conformational change is ligand concentration dependent.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein componentA119Bacillus subtilisMutation(s): 3 
Gene Names: rnpABSSC8_00790
EC: 3.1.26.5
Find proteins for P25814 (Bacillus subtilis (strain 168))
Explore P25814 
Go to UniProtKB:  P25814
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPV
Query on PPV

Download CCD File 
A
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.152α = 90
b = 83.152β = 90
c = 32.236γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-02-28 
  • Released Date: 2014-01-22 
  • Deposition Author(s): Tonthat, N.K.

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references