2CBX

X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with beta-D-erythrofuranosyl- adenosine

• PDB DOI: https://doi.org/10.2210/pdb2CBX/pdb

• Classification: TRANSFERASE
• Organism(s): Streptantibioticus cattleyicolor
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-09 Released: 2007-03-06 
• Deposition Author(s): McEwan, A.R., Cadicamo, C.D., Deng, H., McGlinchey, R.P., Robinson, D.R., O'Hagan, D., Naismith, J.H., Spencer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

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: 1458-1460

• 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: 98.74 kDa 
• Atom Count: 7,260 
• 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
CC5	D [auth A], J [auth B], L [auth C]	BETA-D-ERYTHROFURANOSYL-ADENOSINE C9 H11 N5 O3 DTGVOXMKTYPSSO-NVMQTXNBSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], M [auth C], N [auth C], O [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.815	α = 90
b = 128.017	β = 90
c = 181.028	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: 2007-03-06 
Deposition Author(s): McEwan, A.R., Cadicamo, C.D., Deng, H., McGlinchey, R.P., Robinson, D.R., O'Hagan, D., Naismith, J.H., Spencer, J.

Revision History  

• Version 1.0: 2007-03-06
  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: 2018-03-28
  Changes: Database references, Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description