1FNK

CRYSTAL STRUCTURE ANALYSIS OF CHORISMATE MUTASE MUTANT C88K/R90S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A strategically positioned cation is crucial for efficient catalysis by chorismate mutase.

Kast, P.Grisostomi, C.Chen, I.A.Li, S.Krengel, U.Xue, Y.Hilvert, D.

(2000) J Biol Chem 275: 36832-36838

  • DOI: 10.1074/jbc.M006351200
  • Primary Citation of Related Structures:  
    1FNK, 1FNJ

  • PubMed Abstract: 
  • Combinatorial mutagenesis and in vivo selection experiments previously afforded functional variants of the AroH class Bacillus subtilis chorismate mutase lacking the otherwise highly conserved active site residue Arg(90). Here, we present a detailed kinetic and crystallographic study of several such variants ...

    Combinatorial mutagenesis and in vivo selection experiments previously afforded functional variants of the AroH class Bacillus subtilis chorismate mutase lacking the otherwise highly conserved active site residue Arg(90). Here, we present a detailed kinetic and crystallographic study of several such variants. Removing the arginine side chain (R90G and R90A) reduced catalytic efficiency by more than 5 orders of magnitude. Reintroducing a positive charge to the active site through lysine substitutions restored more than a factor of a thousand in k(cat). Remarkably, the lysine could be placed at position 90 or at the more remote position 88 provided a sterically suitable residue was present at the partner site. Crystal structures of the double mutants C88S/R90K and C88K/R90S show that the lysine adopts an extended conformation that would place its epsilon-ammonium group within hydrogen-bonding distance of the ether oxygen of bound chorismate in the transition state. These results provide support for the hypothesis that developing negative charge in the highly polarized transition state is stabilized electrostatically by a strategically placed cation. The implications of this finding for the mechanism of all natural chorismate mutases and for the design of artificial catalysts are discussed.


    Related Citations: 
    • Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: the importance of electrostatic catalysis
      Kast, P., Asif-Ullah, M., Jiang, N., Hilvert, D.
      (1996) Proc Natl Acad Sci U S A 93: 5043
    • Heavy atom isotope effects reveal a highly polarized transition state for chorismate mutase
      Gustin, D.J., Mattei, P., Kast, P., Wiest, O., Lee, L., Cleland, W.W., Hilvert, D.
      (1999) J Am Chem Soc 121: 1756

    Organizational Affiliation

    Departments of Chemistry and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CHORISMATE MUTASE) A127Bacillus subtilisMutation(s): 3 
EC: 5.4.99.5
Find proteins for P19080 (Bacillus subtilis (strain 168))
Explore P19080 
Go to UniProtKB:  P19080
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.5α = 90
b = 82.5β = 90
c = 42.9γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description