2V7U

X-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g mutant complexed with s-adenosylmethionine and chloride ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1021/ja0731569
  • Primary Citation of Related Structures:  
    2V7T, 2V7U, 2V7V, 2V7W, 2V7X

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-FLUORO-5'-DEOXY ADENOSINE SYNTHETASE
A, B, C
299Streptantibioticus cattleyicolorMutation(s): 1 
EC: 2.5.1.63
UniProt
Find proteins for Q70GK9 (Streptantibioticus cattleyicolor)
Explore Q70GK9 
Go to UniProtKB:  Q70GK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70GK9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.224α = 90
b = 129.377β = 90
c = 183.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-03-28
    Changes: Database references
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description