5UGI

Crystal Structure of Ketosteroid Isomerase D38GF54A mutant from Pseudomonas Testosteroni (tKSI) bound to Equilenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant.

Lamba, V.Yabukarski, F.Herschlag, D.

(2017) J Am Chem Soc 139: 11089-11095

  • DOI: https://doi.org/10.1021/jacs.7b03547
  • Primary Citation of Related Structures:  
    5UGI

  • PubMed Abstract: 

    Control of enzyme activity is fundamental to biology and represents a long-term goal in bioengineering and precision therapeutics. While several powerful molecular strategies have been developed, limitations remain in their generalizability and dynamic range. We demonstrate a control mechanism via separate small molecules that turn on the enzyme (activator) and turn off the activation (blocker). We show that a pocket created near the active site base of the enzyme ketosteriod isomerase (KSI) allows efficient and saturable base rescue when the enzyme's natural general base is removed. Binding a small molecule with similar properties but lacking general-base capability in this pocket shuts off rescue. The ability of small molecules to directly participate in and directly block catalysis may afford a broad controllable dynamic range. This approach may be amenable to numerous enzymes and to engineering and screening approaches to identify activators and blockers with strong, specific binding for engineering and therapeutic applications.


  • Organizational Affiliation

    Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid Delta-isomerase125Comamonas testosteroniMutation(s): 2 
Gene Names: ksi
EC: 5.3.3.1
UniProt
Find proteins for P00947 (Comamonas testosteroni)
Explore P00947 
Go to UniProtKB:  P00947
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00947
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EQU
Query on EQU

Download Ideal Coordinates CCD File 
B [auth A]EQUILENIN
C18 H18 O2
PDRGHUMCVRDZLQ-WMZOPIPTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.777α = 90
b = 60.777β = 90
c = 143.087γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1121778

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description