1DF8

S45A MUTANT OF STREPTAVIDIN IN COMPLEX WITH BIOTIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ser45 plays an important role in managing both the equilibrium and transition state energetics of the streptavidin-biotin system.

Hyre, D.E.Le Trong, I.Freitag, S.Stenkamp, R.E.Stayton, P.S.

(2000) Protein Sci. 9: 878-885

  • DOI: 10.1110/ps.9.5.878

  • PubMed Abstract: 
  • The contribution of the Ser45 hydrogen bond to biotin binding activation and equilibrium thermodynamics was investigated by biophysical and X-ray crystallographic studies. The S45A mutant exhibits a 1,700-fold greater dissociation rate and 907-fold l ...

    The contribution of the Ser45 hydrogen bond to biotin binding activation and equilibrium thermodynamics was investigated by biophysical and X-ray crystallographic studies. The S45A mutant exhibits a 1,700-fold greater dissociation rate and 907-fold lower equilibrium affinity for biotin relative to wild-type streptavidin at 37 degrees C, indicating a crucial role in binding energetics. The crystal structure of the biotin-bound mutant reveals only small changes from the wild-type bound structure, and the remaining hydrogen bonds to biotin retain approximately the same lengths. No additional water molecules are observed to replace the missing hydroxyl, in contrast to the previously studied D128A mutant. The equilibrium deltaG degrees, deltaH degrees, deltaS degrees, deltaC degrees(p), and activation deltaG++ of S45A at 37 degrees C are 13.7+/-0.1 kcal/mol, -21.1+/-0.5 kcal/mol, -23.7+/-1.8 cal/mol K, -223+/-12 cal/mol K, and 20.0+/-2.5 kcal/mol, respectively. Eyring analysis of the large temperature dependence of the S45A off-rate resolves the deltaH++ and deltaS++ of dissociation, 25.8+/-1.2 kcal/mol and 18.7+/-4.3 cal/mol K. The large increases of deltaH++ and deltaS++ in the mutant, relative to wild-type, indicate that Ser45 could form a hydrogen bond with biotin in the wild-type dissociation transition state, enthalpically stabilizing it, and constraining the transition state entropically. The postulated existence of a Ser45-mediated hydrogen bond in the wild-type streptavidin transition state is consistent with potential of mean force simulations of the dissociation pathway and with molecular dynamics simulations of biotin pullout, where Ser45 is seen to form a hydrogen bond with the ureido oxygen as biotin slips past this residue after breaking the native hydrogen bonds.


    Organizational Affiliation

    Department of Bioengineering. University of Washington, Seattle 98195-2125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (STREPTAVIDIN)
A, B
127Streptomyces avidiniiN/A
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

Download SDF File 
Download CCD File 
A, B
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNKd: 1 nM (99) BINDINGDB
BTNΔH: -66.9 - -123 kJ/mol (99) BINDINGDB
BTNKd: 0.2 nM BINDINGMOAD
BTNKd: 0.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 46.200α = 90.00
b = 93.900β = 90.00
c = 104.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
SHELXL-97refinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance