6UFS | pdb_00006ufs

Crystal structure of ketosteroid isomerase from Pseudomonas putida (pKSI) bound to 5 alpha-dihydronandrolone

  • Classification: ISOMERASE
  • Organism(s): Pseudomonas putida
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-09-24 Released: 2020-05-20 
  • Deposition Author(s): Wu, Y., Boxer, S.G.
  • Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase.

Wu, Y.Fried, S.D.Boxer, S.G.

(2020) J Am Chem Soc 142: 9993-9998

  • DOI: https://doi.org/10.1021/jacs.0c00383
  • Primary Citation Related Structures: 
    6UFS

  • PubMed Abstract: 

    Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI's intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction's TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems.


  • Organizational Affiliation
    • Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States.

Macromolecule Content 

  • Total Structure Weight: 30.31 kDa 
  • Atom Count: 2,504 
  • Modeled Residue Count: 256 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Steroid Delta-isomerase
A, B
135Pseudomonas putidaMutation(s): 0 
Gene Names: ksi
EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida)
Explore P07445 
Go to UniProtKB:  P07445
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07445
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q6J
(Subject of Investigation/LOI)

Query on Q6J



Download:Ideal Coordinates CCD File
C [auth B]5alpha-dihydronandrolone
C18 H28 O2
RHVBIEJVJWNXBU-PNOKGRBDSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.661α = 90
b = 73.481β = 90
c = 95.027γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHASERphasing
xia2data reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesGMR35-118044

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description