3UT6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.895 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.febslet.2012.02.039

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase deoD-type
A, B, C
237Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: deoD (pup)
EC: 2.4.2.1
Find proteins for P0ABP8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABP8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FMC
Query on FMC

Download SDF File 
Download CCD File 
A, B, C
(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol
C10 H13 N5 O4
KBHMEHLJSZMEMI-KSYZLYKTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.895 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.769α = 90.00
b = 120.769β = 90.00
c = 239.082γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-11-25 
  • Released Date: 2012-05-23 
  • Deposition Author(s): Stefanic, Z.

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description