2J6W

R164N mutant of the RUNX1 Runt domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Mutation in the S-Switch Region of the Runt Domain Alters the Dynamics of an Allosteric Network Responsible for Cbfbeta Regulation.

Li, Z.Lukasik, S.M.Liu, Y.Grembecka, J.Bielnicka, I.Bushweller, J.H.Speck, N.A.

(2006) J Mol Biol 364: 1073

  • DOI: https://doi.org/10.1016/j.jmb.2006.10.002
  • Primary Citation of Related Structures:  
    2J6W

  • PubMed Abstract: 

    The Runt domain is the DNA binding domain of the core binding factor (CBF) Runx subunits. The CBFs are transcription factors that play critical roles in hematopoiesis, bone, and neuron development in mammals. A common non-DNA binding CBFbeta subunit heterodimerizes with the Runt domain of the Runx proteins and allosterically regulates its affinity for DNA. Previous NMR dynamics studies suggested a model whereby CBFbeta allosterically regulates DNA binding by quenching conformational exchange in the Runt domain, particularly in the S-switch region and the betaE'-F loop. We sought to test this model, and to this end introduced all possible single amino acid substitutions into the S-switch region and the betaE'-F loop, and screened for mutations that enhanced DNA-binding. We demonstrate that one Runt domain mutant, R164N, binds both DNA and CBFbeta with higher affinity, but it is less sensitive to allosteric regulation by CBFbeta. Analysis of NMR relaxation data shows that the chemical exchange exhibited by the wild-type Runt domain is largely quenched by the R164N substitution. These data support a model in which the dynamic behavior of a network of residues connecting the CBFbeta and DNA binding sites on the Runt domain plays a critical role in the mechanism of allosteric regulation. This study provides an important functional link between dynamic behavior and protein allosteric function, consistent with results on other allosterically regulated proteins.


  • Organizational Affiliation

    Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RUNT-RELATED TRANSCRIPTION FACTOR 1
A, B
140Mus musculusMutation(s): 3 
UniProt
Find proteins for Q03347 (Mus musculus)
Explore Q03347 
Go to UniProtKB:  Q03347
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03347
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.948α = 90
b = 46.497β = 90.66
c = 63.552γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKLdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description