Crystal structure of ketosteroid isomerase Y16AD103A from Pseudomonas putida

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase.

Schwans, J.P.Sunden, F.Gonzalez, A.Tsai, Y.Herschlag, D.

(2011) J Am Chem Soc 133: 20052-20055

  • DOI: https://doi.org/10.1021/ja208050t
  • Primary Citation of Related Structures:  
    3T8N, 3T8U

  • PubMed Abstract: 

    Prior site-directed mutagenesis studies in bacterial ketosteroid isomerase (KSI) reported that substitution of both oxyanion hole hydrogen bond donors gives a 10(5)- to 10(8)-fold rate reduction, suggesting that the oxyanion hole may provide the major contribution to KSI catalysis. But these seemingly conservative mutations replaced the oxyanion hole hydrogen bond donors with hydrophobic side chains that could lead to suboptimal solvation of the incipient oxyanion in the mutants, thereby potentially exaggerating the apparent energetic benefit of the hydrogen bonds relative to water-mediated hydrogen bonds in solution. We determined the functional and structural consequences of substituting the oxyanion hole hydrogen bond donors and several residues surrounding the oxyanion hole with smaller residues in an attempt to create a local site that would provide interactions more analogous to those in aqueous solution. These more drastic mutations created an active-site cavity estimated to be ~650 Å(3) and sufficient for occupancy by 15-17 water molecules and led to a rate decrease of only ~10(3)-fold for KSI from two different species, a much smaller effect than that observed from more traditional conservative mutations. The results underscore the strong context dependence of hydrogen bond energetics and suggest that the oxyanion hole provides an important, but moderate, catalytic contribution relative to the interactions in the corresponding solution reaction.

  • Organizational Affiliation

    Department of Biochemistry, Stanford University, Stanford, California 94305, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid Delta-isomeraseA,
C [auth D],
D [auth F]
131Pseudomonas putidaMutation(s): 2 
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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.47 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.514α = 90
b = 76.644β = 63.96
c = 53.06γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description