4L7K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.303 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.USA 110: 11308-11313

  • DOI: 10.1073/pnas.1206710110

  • 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 an ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Steroid Delta-isomerase
A, B, C, D, E, F, G, H, I, J, K, O
125Comamonas testosteroniMutation(s): 1 
Gene Names: ksi
EC: 5.3.3.1
Find proteins for P00947 (Comamonas testosteroni)
Go to UniProtKB:  P00947
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, O
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, D, E, F, J
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.303 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 111.128α = 90.00
b = 111.128β = 90.00
c = 499.813γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-24
    Type: Database references