RCSB PDB - 3ZP4: Arg90Cit chorismate mutase of Bacillus subtilis in complex with a transition state analog

 3ZP4

Arg90Cit chorismate mutase of Bacillus subtilis in complex with a transition state analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.2 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 U S A 111: 17516

  • DOI: https://doi.org/10.1073/pnas.1408512111
  • Primary Citation of Related Structures:  
    3ZO8, 3ZOP, 3ZP4, 3ZP7

  • 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 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

    Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway; and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHORISMATE MUTASE AROH
A, B, C, D, E
127Bacillus subtilisMutation(s): 2 
EC: 5.4.99.5
UniProt
Find proteins for P19080 (Bacillus subtilis (strain 168))
Explore P19080 
Go to UniProtKB:  P19080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19080
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.208α = 97.36
b = 50.842β = 93.18
c = 69.821γ = 100.99
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TSAClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2014-12-03
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Database references
  • Version 1.4: 2014-12-24
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other
  • Version 2.1: 2023-12-20
    Changes: Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary