Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI)

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 

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Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site.

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

(2013) Proc Natl Acad Sci U S A 110: 11308-11313

  • DOI: https://doi.org/10.1073/pnas.1206710110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Although the cation-pi pair, formed between a side chain or substrate cation and the negative electrostatic potential of a pi system on the face of an aromatic ring, has been widely discussed and has been shown to be important in protein structure and protein-ligand interactions, there has been little discussion of the potential structural and functional importance in proteins of the related anion-aromatic pair (i.e., interaction of a negatively charged group with the positive electrostatic potential on the ring edge of an aromatic group). We posited, based on prior structural information, that anion-aromatic interactions between the anionic Asp general base and Phe54 and Phe116 might be used instead of a hydrogen-bond network to position the general base in the active site of ketosteroid isomerase from Comamonas testosteroni as there are no neighboring hydrogen-bonding groups. We have tested the role of the Phe residues using site-directed mutagenesis, double-mutant cycles, and high-resolution X-ray crystallography. These results indicate a catalytic role of these Phe residues. Extensive analysis of the Protein Data Bank provides strong support for a catalytic role of these and other Phe residues in providing anion-aromatic interactions that position anionic general bases within enzyme active sites. Our results further reveal a potential selective advantage of Phe in certain situations, relative to more traditional hydrogen-bonding groups, because it can simultaneously aid in the binding of hydrophobic substrates and positioning of a neighboring general base.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid Delta-isomerase
L [auth O]
125Comamonas testosteroniMutation(s): 1 
Gene Names: ksi
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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth H]
BA [auth C]
BB [auth H]
CA [auth C]
AA [auth C],
AB [auth H],
BA [auth C],
BB [auth H],
CA [auth C],
CB [auth I],
DA [auth C],
DB [auth I],
EB [auth I],
FA [auth D],
GA [auth D],
GB [auth J],
HA [auth D],
HB [auth J],
IA [auth D],
IB [auth K],
JA [auth D],
JB [auth K],
KB [auth K],
LA [auth E],
LB [auth K],
MA [auth E],
MB [auth O],
N [auth A],
NA [auth E],
NB [auth O],
O [auth A],
OA [auth E],
OB [auth O],
P [auth A],
PB [auth O],
Q [auth A],
QA [auth F],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F],
U [auth B],
UA [auth F],
V [auth B],
VA [auth F],
W [auth B],
WA [auth G],
X [auth B],
XA [auth G],
Y [auth C],
YA [auth G],
Z [auth C],
ZA [auth H]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth D],
FB [auth J],
KA [auth E],
M [auth A],
PA [auth F]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.128α = 90
b = 111.128β = 90
c = 499.813γ = 120
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: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations