Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 26.25 kDa 
• Atom Count: 2217 
• Modelled Residue Count: 233 
• Deposited Residue Count: 235 
• Unique protein chains: 1

3UAY

Crystal structure of Bacillus cereus adenosine phosphorylase D204N mutant complexed with adenosine

• PDB DOI: 10.2210/pdb3UAY/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus cereus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-10-22 Released: 2012-02-29 
• Deposition Author(s): Dessanti, P., Zhang, Y., Allegrini, S., Tozzi, M.G., Sgarrella, F., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.152 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Literature

Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase.

Dessanti, P., Zhang, Y., Allegrini, S., Tozzi, M.G., Sgarrella, F., Ealick, S.E.

(2012) Acta Crystallogr D Biol Crystallogr 68: 239-248

• PubMed: 22349225 
• DOI: 10.1107/S090744491200073X
• Primary Citation of Related Structures:  
  3UAV, 3UAW, 3UAX, 3UAY, 3UAZ


• PubMed Abstract: 
  

Purine nucleoside phosphorylases catalyze the phosphorolytic cleavage of the glycosidic bond of purine (2'-deoxy)nucleosides, generating the corresponding free base and (2'-deoxy)-ribose 1-phosphate. Two classes of PNPs have been identified: homotrimers specific for 6-oxopurines and homohexamers that accept both 6-oxopurines and 6-aminopurines. Bacillus cereus adenosine phosphorylase (AdoP) is a hexameric PNP; however, it is highly specific for 6-aminopurines. To investigate the structural basis for the unique substrate specificity of AdoP, the active-site mutant D204N was prepared and kinetically characterized and the structures of the wild-type protein and the D204N mutant complexed with adenosine and sulfate or with inosine and sulfate were determined at high resolution (1.2-1.4 Å). AdoP interacts directly with the preferred substrate through a hydrogen-bond donation from the catalytically important residue Asp204 to N7 of the purine base. Comparison with Escherichia coli PNP revealed a more optimal orientation of Asp204 towards N7 of adenosine and a more closed active site. When inosine is bound, two water molecules are interposed between Asp204 and the N7 and O6 atoms of the nucleoside, thus allowing the enzyme to find alternative but less efficient ways to stabilize the transition state. The mutation of Asp204 to asparagine led to a significant decrease in catalytic efficiency for adenosine without affecting the efficiency of inosine cleavage.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase deoD-type	A	235	Bacillus cereus	Mutation(s): 1  Gene Names: deoD EC: 2.4.2.1
UniProt
Find proteins for Q5EEL8 (Bacillus cereus) Explore Q5EEL8  Go to UniProtKB:  Q5EEL8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	B [auth A]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.152 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.2	α = 90
b = 122.2	β = 90
c = 68.2	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-22 
• Released Date: 2012-02-29 
Deposition Author(s): Dessanti, P., Zhang, Y., Allegrini, S., Tozzi, M.G., Sgarrella, F., Ealick, S.E.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description