1YRY

Crystal structure of human PNP complexed with MESG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine

Silva, R.G., Pereira, J.H., Canduri, F., de Azevedo Jr., W.F., Basso, L.A., Santos, D.S.

(2005) Arch Biochem Biophys 442: 49-58

  • DOI: 10.1016/j.abb.2005.07.021
  • Primary Citation of Related Structures:  
    1YRY

  • PubMed Abstract: 

    • Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation ...

    Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of nucleosides and deoxynucleosides, generating ribose 1-phosphate and the purine base, which is an important step of purine catabolism pathway. The lack of such an activity in humans, owing to a genetic disorder, causes T-cell impairment, and drugs that inhibit this enzyme may have the potential of being utilized as modulators of the immunological system to treat leukemia, autoimmune diseases, and rejection in organ transplantation. Here, we describe kinetics and crystal structure of human PNP in complex with 7-methyl-6-thio-guanosine, a synthetic substrate, which is largely used in activity assays. Analysis of the structure identifies different protein conformational changes upon ligand binding, and comparison of kinetic and structural data permits an understanding of the effects of atomic substitution on key positions of the synthetic substrate and their consequences to enzyme binding and catalysis. Such knowledge may be helpful in designing new PNP inhibitors.

    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
    Organizational Affiliation: 

    Centro de Pesquisas em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, PUCRS, Porto Alegre, RS, Brazil.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA [auth E]289Homo sapiensMutation(s): 0 
Gene Names: PNP, NP
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSG
Query on MSG
Download Ideal Coordinates CCD File 
 E7-METHYL-6-THIO-GUANOSINE
C11 H15 N5 O4 S
RFHIWBUKNJIBSE-KQYNXXCUSA-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: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.99α = 90
b = 138.99β = 90
c = 159.85γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance