2C5B

X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 2'deoxy-5'deoxy-fluoroadenosine.

• PDB DOI: https://doi.org/10.2210/pdb2C5B/pdb

• Classification: TRANSFERASE
• Organism(s): Streptantibioticus cattleyicolor
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-10-26 Released: 2007-02-20 
• Deposition Author(s): McEwan, A.R., Deng, H., McGlinchey, R.P., Robinson, D.A., O'Hagan, D., Naismith, J.H., Spencer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Substrate Specificity in Enzymatic Fluorination. The Fluorinase from Streptomyces Cattleya Accepts 2'-Deoxyadenosine Substrates.

Cobb, S.L., Deng, H., Mcewan, A.R., Naismith, J.H., O'Hagan, D., Robinson, D.A.

(2006) Org Biomol Chem 4: 1458

• PubMed: 16604208 
• DOI: https://doi.org/10.1039/b600574h
• Primary Citation of Related Structures:  
  2C4U, 2C5B, 2CBX, 2CC2


• PubMed Abstract: 
  

  The fluorinase enzyme from Streptomyces cattleya displays an unusual ability in biocatalysis in that it forms a C-F bond. We now report that the enzyme will accept 2'-deoxyadenosine in place of adenosine substrates, and structural evidence reveals a reorganisation in hydrogen bonding to accommodate this substrate series. It emerges from this study that the enzyme does not require a planar ribose conformation of the substrate to catalyse C-F bond formation.

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Organizational Affiliation: 

School of Chemistry, Centre for Biomolecular Sciences, University of St Andrews, Purdie Building, North Haugh, St Andrews, KY16 9ST, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 98.41 kDa 
• Atom Count: 6,937 
• Modelled Residue Count: 873 
• Deposited Residue Count: 897 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE	A, B, C	299	Streptantibioticus cattleyicolor	Mutation(s): 0  EC: 2.5.1.63
UniProt
Find proteins for Q70GK9 (Streptantibioticus cattleyicolor) Explore Q70GK9  Go to UniProtKB:  Q70GK9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5F1	E [auth A], G [auth B], I [auth C]	5'-FLUORO-2',5'-DIDEOXYADENOSINE C10 H12 F N5 O2 QKUCDAPGYBWICH-RRKCRQDMSA-N
MET	D [auth A], F [auth B], H [auth C]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.153	α = 90
b = 129.669	β = 90
c = 183.165	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): McEwan, A.R., Deng, H., McGlinchey, R.P., Robinson, D.A., O'Hagan, D., Naismith, J.H., Spencer, J.

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description