Crystal structure of ketosteroid isomerase from Psedomonas putida complexed with deoxycholate

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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Detection of Large Pka Perturbations of an Inhibitor and a Catalytic Group at an Enzyme Active Site, a Mechanistic Basis for Catalytic Power of Many Enzymes

Ha, N.-C.Kim, M.-S.Lee, W.Choi, K.Y.Oh, B.-H.

(2000) J Biol Chem 275: 41100

  • DOI: https://doi.org/10.1074/jbc.M007561200
  • Primary Citation of Related Structures:  
    1E3R, 1E3V, 1OGX

  • PubMed Abstract: 

    Delta(5)-3-Ketosteroid isomerase catalyzes cleavage and formation of a C-H bond at a diffusion-controlled limit. By determining the crystal structures of the enzyme in complex with each of three different inhibitors and by nuclear magnetic resonance (NMR) spectroscopic investigation, we evidenced the ionization of a hydroxyl group (pK(a) approximately 16.5) of an inhibitor, which forms a low barrier hydrogen bond (LBHB) with a catalytic residue Tyr(14) (pK(a) approximately 11.5), and the protonation of the catalytic residue Asp(38) with pK(a) of approximately 4.5 at pH 6.7 in the interaction with a carboxylate group of an inhibitor. The perturbation of the pK(a) values in both cases arises from the formation of favorable interactions between inhibitors and catalytic residues. The results indicate that the pK(a) difference between catalytic residue and substrate can be significantly reduced in the active site environment as a result of the formation of energetically favorable interactions during the course of enzyme reactions. The reduction in the pK(a) difference should facilitate the abstraction of a proton and thereby eliminate a large fraction of activation energy in general acid/base enzyme reactions. The pK(a) perturbation provides a mechanistic ground for the fast reactivity of many enzymes and for the understanding of how some enzymes are able to extract a proton from a C-H group with a pK(a) value as high as approximately 30.

  • Organizational Affiliation

    National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science and Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
131Pseudomonas putidaMutation(s): 0 
Gene Names: ksi
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DXC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C24 H40 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
DXC PDBBind:  1E3V Kd: 4.57e+4 (nM) from 1 assay(s)
Binding MOAD:  1E3V Kd: 4.57e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.58α = 90
b = 75.21β = 90
c = 96.13γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection