2V7X

X-RAY CRYSTAL STRUCTURE OF 5'-FLUORODEOXYADENOSINE SYNTHASE S158A mutant FROM STREPTOMYCES CATTLEYA COMPLEXED WITH the PRODUCTS, FDA and Met


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of enzymatic fluorination in Streptomyces cattleya.

Zhu, X.Robinson, D.A.McEwan, A.R.O'Hagan, D.Naismith, J.H.

(2007) J. Am. Chem. Soc. 129: 14597-14604

  • DOI: 10.1021/ja0731569
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recently a fluorination enzyme was identified and isolated from Streptomyces cattleya, as the first committed step on the metabolic pathway to the fluorinated metabolites, fluoroacetate and 4-fluorothreonine. This enzyme, 5'-fluoro-5'-deoxy adenosine ...

    Recently a fluorination enzyme was identified and isolated from Streptomyces cattleya, as the first committed step on the metabolic pathway to the fluorinated metabolites, fluoroacetate and 4-fluorothreonine. This enzyme, 5'-fluoro-5'-deoxy adenosine synthetase (FDAS), has been shown to catalyze C-F bond formation by nucleophilic attack of fluoride ion to S-adenosyl-l-methionine (SAM) with the concomitant displacement of l-methionine to generate 5'-fluoro-5'-deoxy adenosine (5'-FDA). Although the structures of FDAS bound to both SAM and products have been solved, the molecular mechanism remained to be elucidated. We now report site-directed mutagenesis studies, structural analyses, and isothermal calorimetry (ITC) experiments. The data establish the key residues required for catalysis and the order of substrate binding. Fluoride ion is not readily distinguished from water by protein X-ray crystallography; however, using chloride ion (also a substrate) with a mutant of low activity has enabled the halide ion to be located in nonproductive co-complexes with SAH and SAM. The kinetic data suggest the positively charged sulfur of SAM is a key requirement in stabilizing the transition state. We propose a molecular mechanism for FDAS in which fluoride weakly associates with the enzyme exchanging two water molecules for protein ligation. The binding of SAM expels remaining water associated with fluoride ion and traps the ion in a pocket positioned to react with SAM, generating l-methionine and 5'-FDA. l-methionine then dissociates from the enzyme followed by 5'-FDA.


    Organizational Affiliation

    Center for Biomolecular Sciences, University of St. Andrews, St. Andrews, KY16 9ST, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
A, B, C
299Streptomyces cattleyaMutation(s): 1 
Gene Names: flA
EC: 2.5.1.63
Find proteins for Q70GK9 (Streptomyces cattleya)
Go to UniProtKB:  Q70GK9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5FD
Query on 5FD

Download SDF File 
Download CCD File 
A, B, C
5'-FLUORO-5'-DEOXYADENOSINE
C10 H14 F N5 O3
VLNOZPDKHNKIIU-SCKUCUMDSA-N
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
A, B, C
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
METKa: 59000 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.575α = 90.00
b = 127.355β = 90.00
c = 180.192γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2018-03-28
    Type: Database references