4BPS

Crystal structure of Chorismatase at 1.08 Angstrom resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.081 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanistic Implications for the Chorismatase Fkbo Based on the Crystal Structure.

Juneja, P.Hubrich, F.Diederichs, K.Welte, W.Andexer, J.N.

(2014) J.Mol.Biol. 426: 105

  • DOI: 10.1016/j.jmb.2013.09.006

  • PubMed Abstract: 
  • Chorismate-converting enzymes are involved in many biosynthetic pathways leading to natural products and can often be used as tools for the synthesis of chemical building blocks. Chorismatases such as FkbO from Streptomyces species catalyse the hydro ...

    Chorismate-converting enzymes are involved in many biosynthetic pathways leading to natural products and can often be used as tools for the synthesis of chemical building blocks. Chorismatases such as FkbO from Streptomyces species catalyse the hydrolysis of chorismate yielding (dihydro)benzoic acid derivatives. In contrast to many other chorismate-converting enzymes, the structure and catalytic mechanism of a chorismatase had not been previously elucidated. Here we present the crystal structure of the chorismatase FkbO in complex with a competitive inhibitor at 1.08Å resolution. FkbO is a monomer in solution and exhibits pseudo-3-fold symmetry; the structure of the individual domains indicates a possible connection to the trimeric RidA/YjgF family and related enzymes. The co-crystallised inhibitor led to the identification of FkbO's active site in the cleft between the central and the C-terminal domains. A mechanism for FkbO is proposed based on both interactions between the inhibitor and the surrounding amino acids and an FkbO structure with chorismate modelled in the active site. We suggest that the methylene group of the chorismate enol ether takes up a proton from an active-site glutamic acid residue, thereby initiating chorismate hydrolysis. A similar chemistry has been described for isochorismatases, albeit implemented in an entirely different protein scaffold. This reaction model is supported by kinetic data from active-site variants of FkbO derived by site-directed mutagenesis.


    Organizational Affiliation

    Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FKBO
A
344Streptomyces hygroscopicusMutation(s): 0 
Gene Names: fkbO
EC: 3.3.2.13
Find proteins for Q9KID9 (Streptomyces hygroscopicus)
Go to UniProtKB:  Q9KID9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3EB
Query on 3EB

Download SDF File 
Download CCD File 
A
3-(2-CARBOXYETHYL)BENZOIC ACID
C10 H10 O4
XUOCLOJWCPUKCS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3EBKi: 1020000 nM BINDINGMOAD
3EBKi: 1020000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.081 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.139α = 90.00
b = 52.250β = 93.35
c = 52.532γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL2MAPphasing
XDSphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references
  • Version 1.2: 2014-01-15
    Type: Atomic model, Database references, Other
  • Version 1.3: 2016-06-29
    Type: Structure summary