3CTK

Crystal structure of the type 1 RIP bouganin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure/function studies on two type 1 ribosome inactivating proteins: Bouganin and lychnin.

Fermani, S.Tosi, G.Farini, V.Polito, L.Falini, G.Ripamonti, A.Barbieri, L.Chambery, A.Bolognesi, A.

(2009) J.Struct.Biol. 168: 278-287

  • DOI: 10.1016/j.jsb.2009.07.010

  • PubMed Abstract: 
  • The three-dimensional structures of two type 1 RIPs, bouganin and lychnin, has been solved. Their adenine polynucleotide glycosylase activity was also determined together with other known RIPs: dianthin 30, PAP-R, momordin I, ricin A chain and sapori ...

    The three-dimensional structures of two type 1 RIPs, bouganin and lychnin, has been solved. Their adenine polynucleotide glycosylase activity was also determined together with other known RIPs: dianthin 30, PAP-R, momordin I, ricin A chain and saporin-S6. Saporin-S6 releases the highest number of adenine molecules from rat ribosomes, and poly(A), while its efficiency is similar to dianthin 30, bouganin and PAP-R on herring sperm DNA. Measures of the protein synthesis inhibitory activity confirmed that saporin-S6 is the most active. The overall structure of bouganin and lychnin is similar to the other considered RIPs and the typical RIP fold is conserved. The superimpositioning of their C(alpha) atoms highlights some differences in the N-terminal and C-terminal domains. A detailed structural analysis indicates that the efficiency of saporin-S6 on various polynucleotides can be ascribed to a negative electrostatic surface potential at the active site and several exposed positively charged residues in the region around that site. These two conditions, not present at the same time in other examined RIPs, could guarantee an efficient interaction with the substrate and an efficient catalysis.


    Related Citations: 
    • New ribosome-inactivating proteins with polynucleotide:adenosine glycosidase and antiviral activities from Basella rubra l. and Bougainvillea spectabilis willd
      Bolognesi, A.,Polito, L.,Olivieri, F.,Valbonesi, P.,Barbieri, L.,Battelli, M.G.,Carusi, M.V.,Benvenuto, E.,Del Vecchio Blanco, F.,Di Maro, A.,Di Loreto, M.,Stirpe, F.
      (1997) Planta 203: 422
    • In vitro anti-tumour activity of anti-CD80 and anti-CD86 immunotoxins containing type 1 ribosome-inactivating proteins
      Bolognesi, A.,Polito, L.,Tazzari, P.L.,Lemoli, R.L.,Lubelli, C.,Fogli, M.,Boon, L.,De Boer, M.,Stirpe, F.
      (2000) Br.J.Haematol. 110: 351


    Organizational Affiliation

    Department of Chemistry "G. Ciamician", Alma Mater Studiorum University of Bologna, Italy. simona.fermani@unibo.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
rRNA N-glycosidase
A
248Bougainvillea spectabilisMutation(s): 0 
EC: 3.2.2.22
Find proteins for Q8W4U4 (Bougainvillea spectabilis)
Go to UniProtKB:  Q8W4U4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.838α = 90.00
b = 77.501β = 90.00
c = 79.383γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Database references