1D6A

STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH GUANINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray crystallographic analysis of the structural basis for the interaction of pokeweed antiviral protein with guanine residues of ribosomal RNA.

Kurinov, I.V.Rajamohan, F.Venkatachalam, T.K.Uckun, F.M.

(1999) Protein Sci. 8: 2399-2405

  • DOI: 10.1110/ps.8.11.2399

  • PubMed Abstract: 
  • Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein (RIP), which enzymatically removes a single adenine base from a conserved, surface exposed loop sequence of ribosomal rRNA. We now present unprecedented experimental evidence that PA ...

    Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein (RIP), which enzymatically removes a single adenine base from a conserved, surface exposed loop sequence of ribosomal rRNA. We now present unprecedented experimental evidence that PAP can release not only adenine but guanine as well from Escherichia coli rRNA, albeit at a rate 20 times slower than for adenine. We also report X-ray structure analysis and supporting modeling studies for the interactions of PAP with guanine. Our modeling studies indicated that PAP can accommodate a guanine base in the active site pocket without large conformational changes. This prediction was experimentally confirmed, since a guanine base was visible in the active site pocket of the crystal structure of the PAP-guanine complex.


    Organizational Affiliation

    Department of Structural Biology, Hughes Institute, Roseville, Minnesota 55113, USA. igor@ih.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POKEWEED ANTIVIRAL PROTEIN
A, B
262Phytolacca americanaGene Names: PAP1
EC: 3.2.2.22
Find proteins for P10297 (Phytolacca americana)
Go to UniProtKB:  P10297
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GUN
Query on GUN

Download SDF File 
Download CCD File 
A, B
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.294α = 68.66
b = 49.411β = 81.04
c = 64.288γ = 63.87
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description