Crystal structure of delta5-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Crystal Structure of Delta-5-3-Ketosteroid Isomerase from Pseudomonas Testosteroni in Complex with Equilenin Settles the Correct Hydrogen Scheme for Transition-State Stabilization

Cho, H.-S.Ha, N.-C.Choi, G.Kim, H.-J.Lee, D.Oh, K.S.Kim, K.S.Lee, W.Choi, K.Y.Oh, B.-H.

(1999) J Biol Chem 274: 32863

  • DOI: https://doi.org/10.1074/jbc.274.46.32863
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Delta(5)-3-Ketosteroid isomerase from Pseudomonas testosteroni has been intensively studied as a prototype to understand an enzyme-catalyzed allylic isomerization. Asp(38) (pK(a) approximately 4.7) was identified as the general base abstracting the steroid C4beta proton (pK(a) approximately 12.7) to form a dienolate intermediate. A key and common enigmatic issue involved in the proton abstraction is the question of how the energy required for the unfavorable proton transfer can be provided at the active site of the enzyme and/or how the thermodynamic barrier can be drastically reduced. Answering this question has been hindered by the existence of two differently proposed enzyme reaction mechanisms. The 2.26 A crystal structure of the enzyme in complex with a reaction intermediate analogue equilenin reveals clearly that both the Tyr(14) OH and Asp(99) COOH provide direct hydrogen bonds to the oxyanion of equilenin. The result negates the catalytic dyad mechanism in which Asp(99) donates the hydrogen bond to Tyr(14), which in turn is hydrogen bonded to the steroid. A theoretical calculation also favors the doubly hydrogen-bonded system over the dyad system. Proton nuclear magnetic resonance analyses of several mutant enzymes indicate that the Tyr(14) OH forms a low barrier hydrogen bond with the dienolic oxyanion of the intermediate.

  • Organizational Affiliation

    Department of Life Science, School of Environmental Engineering, 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, C, D, E
A, B, C, D, E, F
125Comamonas testosteroniMutation(s): 1 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.9α = 90
b = 72.5β = 104.3
c = 80.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-16
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description