1PAG

THE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The 2.5 A structure of pokeweed antiviral protein.

Monzingo, A.F.Collins, E.J.Ernst, S.R.Irvin, J.D.Robertus, J.D.

(1993) J Mol Biol 233: 705-715

  • DOI: 10.1006/jmbi.1993.1547
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The pokeweed antiviral protein (PAP), isolated from the leaves of Phytolacca americana, is one of a family of plant and bacterial ribosome-inhibiting proteins (RIPs) which act as specific N-glycosidases on rRNA. Here we report the three-dimensional s ...

    The pokeweed antiviral protein (PAP), isolated from the leaves of Phytolacca americana, is one of a family of plant and bacterial ribosome-inhibiting proteins (RIPs) which act as specific N-glycosidases on rRNA. Here we report the three-dimensional structure of PAP determined to 2.5 A resolution by X-ray crystallography. After 14 rounds of refinement, the R factor is 0.17 for 5.0 to 2.5 A data. The protein is homologous with the A chain of ricin and exhibits a very similar folding pattern. The positions of key active site residues are also similar. We also report the 2.8 A structure of PAP complexed with a substrate analog, formycin 5'-monophosphate. As seen previously in ricin, the formycin ring is stacked between invariant tyrosines 72 and 123. Arg179 bonds to N-3 which is thought to be important in catalysis.


    Related Citations: 
    • Preliminary X-Ray Diffraction Studies on an Anti-Viral Protein
      Robertus, J.D., Monzingo, A.F., Irvin, J.D.
      (1977) Biochem Biophys Res Commun 74: 775

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas, Austin 78712.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POKEWEED ANTIVIRAL PROTEINA, B262Phytolacca americanaMutation(s): 0 
Gene Names: PAP1
EC: 3.2.2.22
Find proteins for P10297 (Phytolacca americana)
Explore P10297 
Go to UniProtKB:  P10297
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMP
Query on FMP

Download CCD File 
A, B
FORMYCIN-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
PBAHXXBYQACZMA-KSYZLYKTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.4α = 80
b = 50.1β = 113.2
c = 65.2γ = 116.5
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance