1V45

Crystal Structure of human PNP complexed with 3-deoxyguanosine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.263 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of human PNP complexed with ligands.

Canduri, F., Silva, R.G., dos Santos, D.M., Palma, M.S., Basso, L.A., Santos, D.S., de Azevedo Jr., W.F.

(2005) Acta Crystallogr D Biol Crystallogr 61: 856-862

  • DOI: 10.1107/S0907444905005421
  • Primary Citation of Related Structures:  
    1RFG, 1V41, 1V45

  • PubMed Abstract: 

    • Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine-salvage pathway, which allows cells to utilize preformed bases and nucleosides in order to synthesize nucleotides. PNP is specific for purine nucleosides in the beta-configuration and exhibits a strong preference for purines containing a 6-keto group and ribosyl-containing nucleosides relative to the corresponding analogues ...

    Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine-salvage pathway, which allows cells to utilize preformed bases and nucleosides in order to synthesize nucleotides. PNP is specific for purine nucleosides in the beta-configuration and exhibits a strong preference for purines containing a 6-keto group and ribosyl-containing nucleosides relative to the corresponding analogues. PNP was crystallized in complex with ligands and data collection was performed using synchrotron radiation. This work reports the structure of human PNP in complex with guanosine (at 2.80 A resolution), 3'-deoxyguanosine (at 2.86 A resolution) and 8-azaguanine (at 2.85 A resolution). These structures were compared with the PNP-guanine, PNP-inosine and PNP-immucillin-H complexes solved previously.

    Related Citations: 
    • Crystal Structure of Human Purine Nucleoside Phosphorylase at 2.3A Resolution
      De Azevedo Jr., W.F., Canduri, F., Dos Santos, D.M., Silva, R.G., De Oliveira, J.S., De Carvalho, L.P., Basso, L.A., Mendes, M.A., Palma, M.S., Santos, D.S.
      (2003) Biochem Biophys Res Commun 308: 545
    • Crystal structure of human purine nucleoside phosphorylase complexed with acyclovir
      Dos Santos, D.M., Canduri, F., Pereira, J.H., Dias, M.V.B., Silva, R.G., Mendes, M.A., Palma, M.S., Basso, L.A., De Azevedo, W.F., Santos, D.S.
      (2003) Biochem Biophys Res Commun 308: 553
    Organizational Affiliation: 

    Programa de Pós-Graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000, Brazil.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA [auth E]288Homo sapiensMutation(s): 0 
Gene Names: PNP, NP
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00491
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3DG
Query on 3DG
Download Ideal Coordinates CCD File 
E 9-(3-DEOXY-BETA-D-RIBOFURANOSYL)GUANINE
C10 H13 N5 O4
OROIAVZITJBGSM-OBXARNEKSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth E],
C [auth E],
D [auth E]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.263 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.32α = 90
b = 141.32β = 90
c = 162.62γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CCP4data scaling
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-04-16
    Changes: Other, Refinement description