1RQP

Crystal structure and mechanism of a bacterial fluorinating enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and mechanism of a bacterial fluorinating enzyme

Dong, C.Huang, F.Deng, H.Schaffrath, C.Spencer, J.B.O'Hagan, D.Naismith, J.H.

(2004) Nature 427: 561-565

  • DOI: 10.1038/nature02280
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fluorine is the thirteenth most abundant element in the earth's crust, but fluoride concentrations in surface water are low and fluorinated metabolites are extremely rare. The fluoride ion is a potent nucleophile in its desolvated state, but is tight ...

    Fluorine is the thirteenth most abundant element in the earth's crust, but fluoride concentrations in surface water are low and fluorinated metabolites are extremely rare. The fluoride ion is a potent nucleophile in its desolvated state, but is tightly hydrated in water and effectively inert. Low availability and a lack of chemical reactivity have largely excluded fluoride from biochemistry: in particular, fluorine's high redox potential precludes the haloperoxidase-type mechanism used in the metabolic incorporation of chloride and bromide ions. But fluorinated chemicals are growing in industrial importance, with applications in pharmaceuticals, agrochemicals and materials products. Reactive fluorination reagents requiring specialist process technologies are needed in industry and, although biological catalysts for these processes are highly sought after, only one enzyme that can convert fluoride to organic fluorine has been described. Streptomyces cattleya can form carbon-fluorine bonds and must therefore have evolved an enzyme able to overcome the chemical challenges of using aqueous fluoride. Here we report the sequence and three-dimensional structure of the first native fluorination enzyme, 5'-fluoro-5'-deoxyadenosine synthase, from this organism. Both substrate and products have been observed bound to the enzyme, enabling us to propose a nucleophilic substitution mechanism for this biological fluorination reaction.


    Related Citations: 
    • Crystallization and X-ray diffraction of 5'-fluoro-5'-deoxyadenosine synthase, a fluorination enzyme from Streptomyces cattleya
      Dong, C.,Deng, H.,Dorward, M.,Schaffrath, C.,O'Hagan, D.,Naismith, J.H.
      (2003) Acta Crystallogr.,Sect.D 59: 2292


    Organizational Affiliation

    Centre for Biomolecular Sciences, The University of St Andrews, Fife KY16 9ST, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-fluoro-5'-deoxyadenosine synthase
A, B, C
299Streptomyces cattleyaMutation(s): 0 
Gene Names: flA
EC: 2.5.1.63
Find proteins for Q70GK9 (Streptomyces cattleya)
Go to UniProtKB:  Q70GK9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B, C
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.908α = 90.00
b = 130.302β = 90.00
c = 183.435γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
REFMACrefinement
CCP4data scaling
SOLVEphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance