3ZP7

Arg90Cit chorismate mutase of Bacillus subtilis in complex with chorismate and prephenate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Electrostatic Transition State Stabilization Rather Than Reactant Destabilization Provides the Chemical Basis for Efficient Chorismate Mutase Catalysis.

Burschowsky, D.Van Eerde, A.Okvist, M.Kienhofer, A.Kast, P.Hilvert, D.Krengel, U.

(2014) Proc.Natl.Acad.Sci.USA 111: 17516

  • DOI: 10.1073/pnas.1408512111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrate ...

    For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.


    Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland.,Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway; and ute.krengel@kjemi.uio.no kast@org.chem.ethz.ch hilvert@org.chem.ethz.ch.,Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway; and.,Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland ute.krengel@kjemi.uio.no kast@org.chem.ethz.ch hilvert@org.chem.ethz.ch.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHORISMATE MUTASE AROH
A, B, C, D, E, F
127Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: aroH
EC: 5.4.99.5
Find proteins for P19080 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P19080
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ISJ
Query on ISJ

Download SDF File 
Download CCD File 
A, B, C, D
(3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid
Chorismic Acid
C10 H10 O6
WTFXTQVDAKGDEY-HTQZYQBOSA-N
 Ligand Interaction
PRE
Query on PRE

Download SDF File 
Download CCD File 
A, B, C, D
PREPHENIC ACID
C10 H10 O6
FPWMCUPFBRFMLH-XGAOUMNUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CIR
Query on CIR
A, B, C, D, E, F
L-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.245α = 97.51
b = 51.307β = 92.91
c = 70.138γ = 101.11
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Atomic model, Derived calculations
  • Version 1.2: 2014-11-26
    Type: Database references
  • Version 1.3: 2014-12-03
    Type: Database references
  • Version 1.4: 2014-12-10
    Type: Database references
  • Version 1.5: 2014-12-24
    Type: Database references