Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 106.92 kDa 
• Atom Count: 6867 
• Modelled Residue Count: 826 
• Deposited Residue Count: 933 
• Unique protein chains: 1

3GB9

Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoroadenine

• DOI: 10.2210/pdb3GB9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-19 Released: 2009-04-14 
• Deposition Author(s): Sawaya, M.R., Afshar, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine.

Afshar, S., Sawaya, M.R., Morrison, S.L.

(2009) Protein Sci 18: 1107-1114

• PubMed: 19388075 
• DOI: 10.1002/pro.91
• Primary Citation of Related Structures:  
  3GB9, 3GGS


• PubMed Abstract: 
  

A double mutant of human purine nucleoside phosphorylase (hDM) with the amino acid mutations Glu201Gln:Asn243Asp cleaves adenosine-based prodrugs to their corresponding cytotoxic drugs. When fused to an anti-tumor targeting component, hDM is targeted to tumor cells, where it effectively catalyzes phosphorolysis of the prodrug, 2-fluoro-2'-deoxyadenosine (F-dAdo) to the cytotoxic drug, 2-fluoroadenine (F-Ade). This cytotoxicity should be restricted only to the tumor microenvironment, because the endogenously expressed wild type enzyme cannot use adenosine-based prodrugs as substrates. To gain insight into the interaction of hDM with F-dAdo, we have determined the crystal structures of hDM with F-dAdo and F-Ade. The structures reveal that despite the two mutations, the overall fold of hDM is nearly identical to the wild type enzyme. Importantly, the residues Gln201 and Asp243 introduced by the mutation form hydrogen bond contacts with F-dAdo that result in its binding and catalysis. Comparison of substrate and product complexes suggest that the side chains of Gln201 and Asp243 as well as the purine base rotate during catalysis possibly facilitating cleavage of the glycosidic bond. The two structures suggest why hDM, unlike the wild-type enzyme, can utilize F-dAdo as substrate. More importantly, they provide a critical foundation for further optimization of cleavage of adenosine-based prodrugs, such as F-dAdo by mutants of human purine nucleoside phosphorylase.

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Organizational Affiliation: 

Department of Microbiology, Immunology, and Molecular Genetics, UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B, C	311	Homo sapiens	Mutation(s): 2  Gene Names: NP, PNP EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens) Explore P00491  Go to UniProtKB:  P00491
NIH Common Fund Data Resources
PHAROS:  P00491 GTEx:  ENSG00000198805

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2F	D [auth A], DA [auth C], Q [auth B]	2-fluoroadenine C5 H4 F N5 WKMPTBDYDNUJLF-UHFFFAOYSA-N
SO4	AA [auth B],  BA [auth B],  CA [auth B],  E [auth A],  EA [auth C],  F [auth A],  FA [auth C],  G [auth A],  GA [auth C],  H [auth A],  HA [auth C],  I [auth A],  IA [auth C],  J [auth A],  JA [auth C],  K [auth A],  KA [auth C],  L [auth A],  LA [auth C],  M [auth A],  MA [auth C],  N [auth A],  O [auth A],  P [auth A],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	NA [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.791	α = 90
b = 130.648	β = 90
c = 149.177	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-19 
• Released Date: 2009-04-14 
Deposition Author(s): Sawaya, M.R., Afshar, S.

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description