1W01

Crystal structure of mutant enzyme Y57F/D103L of ketosteroid isomerase from Pseudomonas putida biotype B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Double-Mutant Cycle Analysis of a Hydrogen Bond Network in Ketosteroid Isomerase from Pseudomonas Putida Biotype B.

Jang, D.S.Cha, H.J.Cha, S.S.Hong, B.H.Ha, N.C.Lee, J.Y.Oh, B.H.Lee, H.S.Choi, K.Y.

(2004) Biochem J 382: 967

  • DOI: 10.1042/BJ20031871
  • Primary Citation of Related Structures:  
    1W01, 1W00, 1W02, 1VZZ

  • PubMed Abstract: 
  • KSI (ketosteroid isomerase) catalyses an allylic isomerization reaction at a diffusion-controlled rate. A hydrogen bond network, Asp(99).Water(504).Tyr(14).Tyr(55).Tyr(30), connects two critical catalytic residues, Tyr(14) and Asp(99), with Tyr(30), Tyr(55) and a water molecule in the highly apolar active site of the Pseudomonas putida KSI ...

    KSI (ketosteroid isomerase) catalyses an allylic isomerization reaction at a diffusion-controlled rate. A hydrogen bond network, Asp(99).Water(504).Tyr(14).Tyr(55).Tyr(30), connects two critical catalytic residues, Tyr(14) and Asp(99), with Tyr(30), Tyr(55) and a water molecule in the highly apolar active site of the Pseudomonas putida KSI. In order to characterize the interactions among these amino acids in the hydrogen bond network of KSI, double-mutant cycle analysis was performed, and the crystal structure of each mutant protein within the cycle was determined respectively to interpret the coupling energy. The DeltaDeltaG(o) values of Y14F/D99L (Tyr(14)-->Phe/Asp(99)-->Leu) KSI, 25.5 kJ/mol for catalysis and 28.9 kJ/mol for stability, were smaller than the sums (i.e. 29.7 kJ/mol for catalysis and 34.3 kJ/mol for stability) for single mutant KSIs respectively, indicating that the effect of the Y14F/D99L mutation was partially additive for both catalysis and stability. The partially additive effect of the Y14F/D99L mutation suggests that Tyr(14) and Asp(99) should interact positively for the stabilization of the transition state during the catalysis. The crystal structure of Y14F/D99L KSI indicated that the Y14F/D99L mutation increased the hydrophobic interaction while disrupting the hydrogen bond network. The DeltaDeltaG(o) values of both Y30F/D99L and Y55F/D99L KSIs for the catalysis and stability were larger than the sum of single mutants, suggesting that either Tyr(30) and Asp(99) or Tyr(55) and Asp(99) should interact negatively for the catalysis and stability. These synergistic effects of both Y30F/D99L and Y55F/D99L mutations resulted from the disruption of the hydrogen bond network. The synergistic effect of the Y55F/D99L mutation was larger than that of the Y30F/D99L mutation, since the former mutation impaired the proper positioning of a critical catalytic residue, Tyr(14), involved in the catalysis of KSI. The present study can provide insight into interpreting the coupling energy measured by double-mutant cycle analysis based on the crystal structures of the wild-type and mutant proteins.


    Related Citations: 
    • Contribution of the Hydrogen-Bond Network Involving a Tyrosine Triad in the Active Site to the Structure and Function of a Highly Proficient Ketosteroid Isomerase from Pseudomonas Putida Biotype B
      Kim, D.H., Jang, D.S., Nam, G.H., Choi, G., Kim, J.S., Ha, N.C., Kim, M.S., Oh, B.H., Choi, K.Y.
      (2000) Biochemistry 39: 4581
    • Crystal Structure of Delta(5)-3-Ketosteroid Isomerase from Pseudomonas Testosteroni in Complex with Equilenin Settles the Correct Hydrogen Bonding 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
    • Crystal Structure and Enzyme Mechanism of Delta(5)-3-Ketosteroid Isomerase from Pseudomonas Testosteroni
      Cho, H.S., Choi, G., Choi, K.Y., Oh, B.H.
      (1998) Biochemistry 37: 8325
    • High-Resolution Crystal Structures of Delta(5)-3-Ketosteroid Isomerase with and without a Reaction Intermediate Analogue
      Kim, S.W., Cha, S.S., Cho, H.S., Kim, J.S., Ha, N.C., Cho, M.J., Joo, S., Kim, K.K., Choi, K.Y., Oh, B.H.
      (1997) Biochemistry 36: 14030

    Organizational Affiliation

    National Research Laboratory of Protein Folding and Engineering, Division of Molecular Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, South Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
STEROID DELTA-ISOMERASEA, B131Pseudomonas putidaMutation(s): 2 
Gene Names: ksi
EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida)
Explore P07445 
Go to UniProtKB:  P07445
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.496α = 90
b = 75.942β = 90
c = 92.312γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2004-05-30 
  • Released Date: 2004-07-08 
  • Deposition Author(s): Jang, D.S., Choi, K.Y.

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-08
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance