Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 109.63 kDa 
• Atom Count: 7126 
• Modelled Residue Count: 859 
• Deposited Residue Count: 972 
• Unique protein chains: 1

4EB8

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate

• PDB DOI: 10.2210/pdb4EB8/pdb

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


• Deposited: 2012-03-23 Released: 2013-02-06 
• Deposition Author(s): Ho, M.C., Haapalainen, A.M., Suarez, J.J., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Catalytic Site Conformations in Human PNP by (19)F-NMR and Crystallography.

Suarez, J., Haapalainen, A.M., Cahill, S.M., Ho, M.C., Yan, F., Almo, S.C., Schramm, V.L.

(2013) Chem Biol 20: 212-222

• PubMed: 23438750 
• DOI: 10.1016/j.chembiol.2013.01.009
• Primary Citation of Related Structures:  
  4EAR, 4EB8, 4ECE, 4GKA


• PubMed Abstract: 
  

Purine nucleoside phosphorylase (PNP) is a target for leukemia, gout, and autoimmune disorders. Dynamic motion of catalytic site loops has been implicated in catalysis, but experimental evidence was lacking. We replaced catalytic site groups His257 or His64 with 6-fluoro-tryptophan (6FW) as site-specific NMR probes. Conformational adjustments in the 6FW-His257-helical and His64-6FW-loop regions were characterized in PNP phosphate-bound enzyme and in complexes with catalytic site ligands, including transition state analogs. Chemical shift and line-shape changes associated with these complexes revealed dynamic coexistence of several conformational states in these regions in phosphate-bound enzyme and altered or single conformations in other complexes. These conformations were also characterized by X-ray crystallography. Specific (19)F-Trp labels and X-ray crystallography provide multidimensional characterization of conformational states for free, catalytic, and inhibited complexes of human PNP.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B, C	324	Homo sapiens	Mutation(s): 5  Gene Names: NP, PNP, X00737.1 EC: 2.4.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00491 (Homo sapiens) Explore P00491  Go to UniProtKB:  P00491
PHAROS:  P00491 GTEx:  ENSG00000198805

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM5	E [auth A], G [auth B], J [auth C]	2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one C12 H17 N5 O3 GSPTUGDLYPMLCQ-SFYZADRCSA-N
PO4	D [auth A], F [auth B], I [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	H [auth B], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IM5	PDBBind:  4EB8	Ki: 0.15 (nM) from 1 assay(s)
	BindingDB:  4EB8	Ki: min: 0.16, max: 7 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.752	α = 90
b = 131.035	β = 90
c = 137.503	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-23 
• Released Date: 2013-02-06 
Deposition Author(s): Ho, M.C., Haapalainen, A.M., Suarez, J.J., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Database references
• Version 1.2: 2013-03-13
  Changes: Database references