3UT6

Crystal structure of E. Coli PNP complexed with PO4 and formycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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This is version 1.2 of the entry. See complete history


Literature

New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A.

Stefanic, Z.Narczyk, M.Mikleusevic, G.Wielgus-Kutrowska, B.Bzowska, A.Luic, M.

(2012) FEBS Lett 586: 967-971

  • DOI: https://doi.org/10.1016/j.febslet.2012.02.039
  • Primary Citation of Related Structures:  
    3UT6

  • PubMed Abstract: 

    Purine nucleoside phosphorylase (PNP) from Escherichia coli is a homohexamer that catalyses the phosphorolytic cleavage of the glycosidic bond of purine nucleosides. The first crystal structure of the ternary complex of this enzyme (with a phosphate ion and formycin A), which is biased by neither the presence of an inhibitor nor sulfate as a precipitant, is presented. The structure reveals, in some active sites, an unexpected and never before observed binding site for phosphate and exhibits a stoichiometry of two phosphate molecules per enzyme subunit. Moreover, in these active sites, the phosphate and nucleoside molecules are found not to be in direct contact. Rather, they are bridged by three water molecules that occupy the "standard" phosphate binding site.


  • Organizational Affiliation

    Rudjer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase deoD-type
A, B, C
237Escherichia coli K-12Mutation(s): 0 
EC: 2.4.2.1
UniProt
Find proteins for P0ABP8 (Escherichia coli (strain K12))
Explore P0ABP8 
Go to UniProtKB:  P0ABP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABP8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.769α = 90
b = 120.769β = 90
c = 239.082γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2012-05-23 
  • Deposition Author(s): Stefanic, Z.

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations