3T6L

Y54F mutant of core streptavidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Second-Contact Shell Mutation Diminishes Streptavidin-Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics.

Baugh, L.Le Trong, I.Cerutti, D.S.Mehta, N.Gulich, S.Stayton, P.S.Stenkamp, R.E.Lybrand, T.P.

(2012) Biochemistry 51: 597-607

  • DOI: 10.1021/bi201221j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report a point mutation in the second contact shell of the high-affinity streptavidin-biotin complex that appears to reduce binding affinity through transmitted effects on equilibrium dynamics. The Y54F streptavidin mutation causes a 75-fold loss ...

    We report a point mutation in the second contact shell of the high-affinity streptavidin-biotin complex that appears to reduce binding affinity through transmitted effects on equilibrium dynamics. The Y54F streptavidin mutation causes a 75-fold loss of binding affinity with 73-fold faster dissociation, a large loss of binding enthalpy (ΔΔH = 3.4 kcal/mol at 37 °C), and a small gain in binding entropy (TΔΔS = 0.7 kcal/mol). The removed Y54 hydroxyl is replaced by a water molecule in the bound structure, but there are no observable changes in structure in the first contact shell and no additional changes surrounding the mutation. Molecular dynamics simulations reveal a large increase in the atomic fluctuation amplitudes for W79, a key biotin contact residue, compared to the fluctuation amplitudes in the wild-type. The increased W79 atomic fluctuation amplitudes are caused by loss of water-mediated hydrogen bonds between the Y54 hydroxyl group and peptide backbone atoms in and near W79. We propose that the increased atomic fluctuation amplitudes diminish the integrity of the W79-biotin interaction and represents a loosening of the "tryptophan collar" that is critical to the slow dissociation and high affinity of streptavidin-biotin binding. These results illustrate how changes in protein dynamics distal to the ligand binding pocket can have a profound impact on ligand binding, even when equilibrium structure is unperturbed.


    Organizational Affiliation

    Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A
127Streptomyces avidiniiMutation(s): 1 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.135 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 57.273α = 90.00
b = 57.273β = 90.00
c = 171.715γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
XDSdata scaling
Blu-Icedata collection
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-02-08
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description