3VGN

Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 3-fluoro-4-nitrophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Sigala, P.A.Fafarman, A.T.Schwans, J.P.Fried, S.D.Fenn, T.D.Caaveiro, J.M.M.Pybus, B.Ringe, D.Petsko, G.A.Boxer, S.G.Herschlag, D.

(2013) Proc.Natl.Acad.Sci.USA 110: E2552-E2561

  • DOI: 10.1073/pnas.1302191110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond ...

    Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol-Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations.


    Organizational Affiliation

    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Steroid Delta-isomerase
A, B
131Pseudomonas putidaMutation(s): 1 
Gene Names: ksi
EC: 5.3.3.1
Find proteins for P07445 (Pseudomonas putida)
Go to UniProtKB:  P07445
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FNN
Query on FNN

Download SDF File 
Download CCD File 
A, B
3-fluoro-4-nitrophenol
C6 H4 F N O3
CSSGKHVRDGATJL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.483α = 90.00
b = 72.315β = 90.00
c = 95.282γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2013-07-17
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description